Inference and Analysis of Synteny Networks with syntenet

Fabricio Almeida-Silva

VIB-UGent Center for Plant Systems Biology

Acknowledgements

People involved in this work:

  • Tao Zhao and M. Eric Schranz
  • Yves Van de Peer

Funding:

  • ERC
  • UGent
  • Max Planck Society

Background

Synteny or colinearity: preservation of gene content and order between different genomic segments.

Pairwise comparisons can be both intraspecies and interspecies.

Intraspecies synteny detection

Typically used to:

  1. Detect whole-genome duplication (WGD) events;
  2. Explore population structure and genomic rearrangements.

Interspecies synteny detection

Typically used to explore:

  1. Divergence between species;
  2. Evolution of gene families and traits of interest;
  3. Genomic rearrangements.

The problem

When comparing multiple species, synteny analyses are hard to interpret and visualize.

The solution

Network representation of synteny: nodes represent genes, which are connected if they are in the same syntenic block.

History of synteny networks

Proposal and first description of the method.

History of synteny networks

Application of synteny networks to study the evolution of MADS-box transcription factors in angiosperms.

History of synteny networks

Application of synteny networks to explore global patterns in mammalian and angiosperm genomes.

History of synteny networks

Extension of method: inferring phylogenies from synteny networks.

The reproducibility problem

Code were available, but not designed to be distributed:

  • Several separate .sh and .R scripts;
  • Users had to process the data by themselves first (not trivial);
  • Application to new data sets required editing lines of the source code.

syntenet to the rescue!

An R/Bioconductor package to infer synteny network from whole-genome protein sequence data.

Anchor pairs are interpreted as linked nodes of an undirected unweighted graph.

Features:

  1. Synteny detection using a native implementation of the MCScanX algorithm (C++ ported to R with Rcpp);
  2. Synteny network inference;
  3. Network clustering using the Infomap algorithm;
  4. Phylogenomic profiling - matrix \(m_{ij}\) with the number of genes from cluster \(j\) in species \(i\);
  5. Microsynteny-based phylogeny reconstruction with maximum likelihood (using IQTREE2).

syntenet workflow

Further reading

Shall we see it in action?

Installation

From Bioconductor:

BiocManager::install(version='devel')
BiocManager::install("syntenet")


From GitHub:

remotes::install_github("almeidasilvaf/syntenet")

Example data set

Data: Whole-genome protein sequences and gene ranges for Chlorophyta algae + Physcomitrium patens as an outgroup.

Source: Pico-PLAZA 3.0

Where to find: the data/ directory in the GitHub repo associated with this presentation.

data
├── annotation.rda
├── cds.rda
├── clusters.rda
├── data_acquisition.Rmd
├── diamond_list.rda
├── profiles.rda
└── proteomes.rda
  1. annotation.rda: GRangesList object with gene ranges.
  2. proteomes.rda: List of AAStringSet objects.

Example data set: annotation

load(here::here("data", "annotation.rda"))

# Inspect data
names(annotation)
 [1] "Aprotothecoides"   "Helicosporidiumsp" "Chlorellasp"      
 [4] "PicRCC4223"        "PicSE3"            "Asterochlorissp"  
 [7] "Csubellipsoidea"   "Creinhardtii"      "Vcarteri"         
[10] "Bprasinos"         "Otauri"            "Osp"              
[13] "Olucimarinus"      "Omediterraneus"    "Msp"              
[16] "Mpusilla"          "Ppatens"          
head(annotation$Aprotothecoides)
GRanges object with 6 ranges and 2 metadata columns:
                    seqnames      ranges strand |     type     gene_id
                       <Rle>   <IRanges>  <Rle> | <factor> <character>
  [1] contig_KL662078-KL66.. 10089-11286      + |     gene  AP00G46350
  [2] contig_KL662078-KL66.. 11827-12024      - |     gene  AP00G46360
  [3] contig_KL662078-KL66.. 12792-14704      + |     gene  AP00G46370
  [4] contig_KL662078-KL66.. 14870-15959      + |     gene  AP00G46380
  [5] contig_KL662078-KL66.. 16290-17247      - |     gene  AP00G46390
  [6] contig_KL662078-KL66.. 18009-20887      + |     gene  AP00G46400
  -------
  seqinfo: 102 sequences from an unspecified genome; no seqlengths

Example data set: proteomes

load(here::here("data", "proteomes.rda"))

# Inspect data
names(proteomes)
 [1] "Aprotothecoides"   "Helicosporidiumsp" "Chlorellasp"      
 [4] "PicRCC4223"        "PicSE3"            "Asterochlorissp"  
 [7] "Csubellipsoidea"   "Creinhardtii"      "Vcarteri"         
[10] "Bprasinos"         "Otauri"            "Osp"              
[13] "Olucimarinus"      "Omediterraneus"    "Msp"              
[16] "Mpusilla"          "Ppatens"          
head(proteomes$Aprotothecoides)
AAStringSet object of length 6:
    width seq                                               names               
[1]   177 MEGVHRQLLETTTQWNGDQVAPL...LALYGLIVGIILASKAGTATPI* AP00G00010
[2]   514 MLAVLARRTGGARFPLSSLNLVV...MLGGVGKEMAMMRRELRRRLLG* AP00G00020
[3]   416 MEAETAQPGDETPGTTAHMRDPA...RSVDGWCTAERRSKRRSWKAKS* AP00G00030
[4]   362 MEALSGTRASFAGATHAFTARKL...NRKRQAKITTELSEIVAGASSV* AP00G00040
[5]   310 MSFVTVGGEASSRPTFFELVAAD...GACPVTLEPVKLEDIWRLYPGM* AP00G00050
[6]   277 MANLFINLPKPCHWQLCTDALRA...WTIEEVLPDGCAGPDLPEEIIL* AP00G00060

A quick check before starting

To enter the workflow, data must satisfy 3 conditions:

  1. Names of list elements in proteomes and annotation match;
  2. Number of sequences in proteomes is not greater than the number of genes in annotation (i.e., primary transcripts only);
  3. Sequence names in proteomes match gene names in annotation.

A quick check before starting

The check can be performed with check_input():

library(syntenet)
check_input(proteomes, annotation)
[1] TRUE

Data preprocessing

The protein sequences and gene ranges are processed to:

  1. Remove period+number from sequence IDs (typically indicate isoforms), e.g.:
    • AT1G01010.1 → AT1G01010
  2. Add unique species ID to each gene and chromosome, e.g.:
    • AT1G01010 → Atha_AT1G01010
    • Chr1 → Atha_Chr1
  3. Remove strings representing stop codons (e.g., * at the end);
  4. Clean each GRanges object to keep only seqnames, ranges, and gene ID.

Data preprocessing

Data preprocessing can be performed with process_input().

pdata <- process_input(proteomes, annotation)
dplyr::glimpse(pdata)
List of 2
 $ seq       :List of 17
  ..$ Aprotothecoides  :Formal class 'AAStringSet' [package "Biostrings"] with 5 slots
  ..$ Helicosporidiumsp:Formal class 'AAStringSet' [package "Biostrings"] with 5 slots
  ..$ Chlorellasp      :Formal class 'AAStringSet' [package "Biostrings"] with 5 slots
  ..$ PicRCC4223       :Formal class 'AAStringSet' [package "Biostrings"] with 5 slots
  ..$ PicSE3           :Formal class 'AAStringSet' [package "Biostrings"] with 5 slots
  ..$ Asterochlorissp  :Formal class 'AAStringSet' [package "Biostrings"] with 5 slots
  ..$ Csubellipsoidea  :Formal class 'AAStringSet' [package "Biostrings"] with 5 slots
  ..$ Creinhardtii     :Formal class 'AAStringSet' [package "Biostrings"] with 5 slots
  ..$ Vcarteri         :Formal class 'AAStringSet' [package "Biostrings"] with 5 slots
  ..$ Bprasinos        :Formal class 'AAStringSet' [package "Biostrings"] with 5 slots
  ..$ Otauri           :Formal class 'AAStringSet' [package "Biostrings"] with 5 slots
  ..$ Osp              :Formal class 'AAStringSet' [package "Biostrings"] with 5 slots
  ..$ Olucimarinus     :Formal class 'AAStringSet' [package "Biostrings"] with 5 slots
  ..$ Omediterraneus   :Formal class 'AAStringSet' [package "Biostrings"] with 5 slots
  ..$ Msp              :Formal class 'AAStringSet' [package "Biostrings"] with 5 slots
  ..$ Mpusilla         :Formal class 'AAStringSet' [package "Biostrings"] with 5 slots
  ..$ Ppatens          :Formal class 'AAStringSet' [package "Biostrings"] with 5 slots
 $ annotation:List of 17
  ..$ Aprotothecoides  :Formal class 'GRanges' [package "GenomicRanges"] with 7 slots
  ..$ Helicosporidiumsp:Formal class 'GRanges' [package "GenomicRanges"] with 7 slots
  ..$ Chlorellasp      :Formal class 'GRanges' [package "GenomicRanges"] with 7 slots
  ..$ PicRCC4223       :Formal class 'GRanges' [package "GenomicRanges"] with 7 slots
  ..$ PicSE3           :Formal class 'GRanges' [package "GenomicRanges"] with 7 slots
  ..$ Asterochlorissp  :Formal class 'GRanges' [package "GenomicRanges"] with 7 slots
  ..$ Csubellipsoidea  :Formal class 'GRanges' [package "GenomicRanges"] with 7 slots
  ..$ Creinhardtii     :Formal class 'GRanges' [package "GenomicRanges"] with 7 slots
  ..$ Vcarteri         :Formal class 'GRanges' [package "GenomicRanges"] with 7 slots
  ..$ Bprasinos        :Formal class 'GRanges' [package "GenomicRanges"] with 7 slots
  ..$ Otauri           :Formal class 'GRanges' [package "GenomicRanges"] with 7 slots
  ..$ Osp              :Formal class 'GRanges' [package "GenomicRanges"] with 7 slots
  ..$ Olucimarinus     :Formal class 'GRanges' [package "GenomicRanges"] with 7 slots
  ..$ Omediterraneus   :Formal class 'GRanges' [package "GenomicRanges"] with 7 slots
  ..$ Msp              :Formal class 'GRanges' [package "GenomicRanges"] with 7 slots
  ..$ Mpusilla         :Formal class 'GRanges' [package "GenomicRanges"] with 7 slots
  ..$ Ppatens          :Formal class 'GRanges' [package "GenomicRanges"] with 7 slots

Similarity search

To detect synteny, you need a list of data frames with the tabular output of DIAMOND, BLASTp or similar programs. It can be obtained by:

  1. Exporting pdata$seq to FASTA files and using them as input to your favorite similarity search program;
  2. Using syntenet’s function run_diamond(), a wrapper that runs DIAMOND from the R session and parses the output as a list of data frames (recommended).

Important

The code below takes ~4-5 minutes to run.

if(diamond_is_installed()) {
    diamond_list <- run_diamond(pdata$seq)
}

Similarity search

To save time, we will load pre-computed output from run_diamond().

load(here::here("data", "diamond_list.rda"))

dplyr::glimpse(diamond_list)
List of 289
 $ Aprotothecoides_Aprotothecoides    :'data.frame':    11194 obs. of  12 variables:
  ..$ query        : chr [1:11194] "Apro_AP00G00010" "Apro_AP00G00020" "Apro_AP00G00030" "Apro_AP00G00040" ...
  ..$ db           : chr [1:11194] "Apro_AP00G00010" "Apro_AP00G00020" "Apro_AP00G00030" "Apro_AP00G00040" ...
  ..$ perc_identity: num [1:11194] 100 100 100 100 30.1 100 100 34.6 41.8 100 ...
  ..$ length       : int [1:11194] 176 513 415 361 329 309 276 81 67 631 ...
  ..$ mismatches   : int [1:11194] 0 0 0 0 170 0 0 48 33 0 ...
  ..$ gap_open     : int [1:11194] 0 0 0 0 7 0 0 2 1 0 ...
  ..$ qstart       : int [1:11194] 1 1 1 1 35 1 1 86 87 1 ...
  ..$ qend         : int [1:11194] 176 513 415 361 361 309 276 163 147 631 ...
  ..$ tstart       : int [1:11194] 1 1 1 1 42 1 1 5 531 1 ...
  ..$ tend         : int [1:11194] 176 513 415 361 312 309 276 83 597 631 ...
  ..$ evalue       : num [1:11194] 9.73e-117 0.00 7.79e-304 6.43e-246 3.63e-24 ...
  ..$ bitscore     : num [1:11194] 326 994 819 668 99 ...
 $ Aprotothecoides_Asterochlorissp    :'data.frame':    8836 obs. of  12 variables:
  ..$ query        : chr [1:8836] "Apro_AP00G00010" "Apro_AP00G00010" "Apro_AP00G00020" "Apro_AP00G00030" ...
  ..$ db           : chr [1:8836] "Aste_AC00G25790" "Aste_AC00G25800" "Aste_AC00G25800" "Aste_AC00G51960" ...
  ..$ perc_identity: num [1:8836] 72.8 72.8 47.9 54.5 67 30.5 47.6 45.2 38.6 43.5 ...
  ..$ length       : int [1:8836] 184 184 497 77 352 328 233 126 83 69 ...
  ..$ mismatches   : int [1:8836] 28 28 197 15 112 177 95 68 44 36 ...
  ..$ gap_open     : int [1:8836] 1 1 3 3 4 8 5 1 2 1 ...
  ..$ qstart       : int [1:8836] 14 14 77 123 8 34 1 152 87 84 ...
  ..$ qend         : int [1:8836] 175 175 511 180 359 361 212 276 162 149 ...
  ..$ tstart       : int [1:8836] 3 3 756 10 22 49 1 215 6 3 ...
  ..$ tend         : int [1:8836] 186 186 1252 85 369 325 227 340 88 71 ...
  ..$ evalue       : num [1:8836] 4.41e-82 5.13e-74 5.39e-138 5.15e-12 1.29e-155 ...
  ..$ bitscore     : num [1:8836] 239 239 428 65.9 440 107 156 115 54.7 53.9 ...
 $ Aprotothecoides_Bprasinos          :'data.frame':    5892 obs. of  12 variables:
  ..$ query        : chr [1:5892] "Apro_AP00G00010" "Apro_AP00G00010" "Apro_AP00G00010" "Apro_AP00G00040" ...
  ..$ db           : chr [1:5892] "Bpra_BPRRCC1105_02G03480" "Bpra_BPRRCC1105_14G02230" "Bpra_BPRRCC1105_15G00560" "Bpra_BPRRCC1105_02G04820" ...
  ..$ perc_identity: num [1:5892] 71.5 49.4 34.6 53.3 29.3 47.8 38.9 45 39.1 56.5 ...
  ..$ length       : int [1:5892] 172 154 159 345 338 69 72 60 64 678 ...
  ..$ mismatches   : int [1:5892] 45 76 98 156 182 35 41 32 38 247 ...
  ..$ gap_open     : int [1:5892] 2 1 2 3 7 1 1 1 1 6 ...
  ..$ qstart       : int [1:5892] 3 16 23 17 24 87 86 87 87 1 ...
  ..$ qend         : int [1:5892] 174 169 175 361 361 154 154 146 149 631 ...
  ..$ tstart       : int [1:5892] 19 4 61 75 44 141 6 5 155 1 ...
  ..$ tend         : int [1:5892] 186 155 219 414 324 209 77 63 218 677 ...
  ..$ evalue       : num [1:5892] 9.84e-72 7.13e-44 1.60e-20 2.99e-114 3.60e-24 ...
  ..$ bitscore     : num [1:5892] 213 141 83.2 337 99.8 63.5 55.1 45.8 47 646 ...
 $ Aprotothecoides_Chlorellasp        :'data.frame':    9477 obs. of  12 variables:
  ..$ query        : chr [1:9477] "Apro_AP00G00010" "Apro_AP00G00010" "Apro_AP00G00020" "Apro_AP00G00040" ...
  ..$ db           : chr [1:9477] "Chlo_CNC64A_009G01580" "Chlo_CNC64A_008G00940" "Chlo_CNC64A_009G01590" "Chlo_CNC64A_009G01480" ...
  ..$ perc_identity: num [1:9477] 91 32.9 50.7 45.3 30.9 48.6 37.5 43.1 36.8 57.2 ...
  ..$ length       : int [1:9477] 167 158 517 340 204 389 80 51 76 673 ...
  ..$ mismatches   : int [1:9477] 15 99 173 67 111 117 46 28 43 172 ...
  ..$ gap_open     : int [1:9477] 0 3 5 2 7 5 2 1 2 6 ...
  ..$ qstart       : int [1:9477] 9 20 77 22 35 1 87 97 90 4 ...
  ..$ qend         : int [1:9477] 175 170 511 361 228 306 163 146 160 631 ...
  ..$ tstart       : int [1:9477] 1 38 79 19 40 1 6 1 104 4 ...
  ..$ tend         : int [1:9477] 167 195 595 239 223 389 84 51 179 605 ...
  ..$ evalue       : num [1:9477] 2.52e-100 1.86e-17 3.38e-162 2.28e-73 5.06e-16 ...
  ..$ bitscore     : num [1:9477] 285 74.7 472 226 75.5 301 52.4 45.4 45.8 677 ...
 $ Aprotothecoides_Creinhardtii       :'data.frame':    8799 obs. of  12 variables:
  ..$ query        : chr [1:8799] "Apro_AP00G00010" "Apro_AP00G00020" "Apro_AP00G00020" "Apro_AP00G00030" ...
  ..$ db           : chr [1:8799] "Crei_CR06G02070" "Crei_CR16G01480" "Crei_CR01G08000" "Crei_CR06G05630" ...
  ..$ perc_identity: num [1:8799] 72.5 48.8 46.7 56.3 63 31.6 45 44.3 44.4 37.1 ...
  ..$ length       : int [1:8799] 167 242 214 48 335 329 220 70 63 97 ...
  ..$ mismatches   : int [1:8799] 42 88 107 21 120 194 106 37 35 49 ...
  ..$ gap_open     : int [1:8799] 2 2 2 0 3 8 5 1 0 3 ...
  ..$ qstart       : int [1:8799] 5 305 305 133 25 34 3 87 87 82 ...
  ..$ qend         : int [1:8799] 171 510 511 180 359 361 211 154 149 172 ...
  ..$ tstart       : int [1:8799] 4 596 371 86 24 42 2 6 8 467 ...
  ..$ tend         : int [1:8799] 166 837 584 133 354 340 217 75 70 557 ...
  ..$ evalue       : num [1:8799] 1.32e-69 3.70e-58 4.51e-51 2.62e-09 2.20e-134 ...
  ..$ bitscore     : num [1:8799] 208 206 183 59.3 387 109 154 60.1 54.7 55.1 ...
 $ Aprotothecoides_Csubellipsoidea    :'data.frame':    8763 obs. of  12 variables:
  ..$ query        : chr [1:8763] "Apro_AP00G00010" "Apro_AP00G00020" "Apro_AP00G00030" "Apro_AP00G00040" ...
  ..$ db           : chr [1:8763] "Csub_CV00G37560" "Csub_CV00G37570" "Csub_CV00G37350" "Csub_CV00G37370" ...
  ..$ perc_identity: num [1:8763] 78.9 47.4 60.4 70.3 34.3 40.4 45.3 40.6 43.8 65.6 ...
  ..$ length       : int [1:8763] 175 468 48 323 329 384 150 69 64 684 ...
  ..$ mismatches   : int [1:8763] 36 181 19 94 163 148 72 38 33 180 ...
  ..$ gap_open     : int [1:8763] 1 4 0 2 10 6 1 2 2 6 ...
  ..$ qstart       : int [1:8763] 1 109 133 37 34 1 137 70 87 1 ...
  ..$ qend         : int [1:8763] 175 511 180 359 361 306 276 136 147 631 ...
  ..$ tstart       : int [1:8763] 1 1 144 47 47 1 236 162 11 1 ...
  ..$ tend         : int [1:8763] 174 468 191 367 323 381 385 229 74 682 ...
  ..$ evalue       : num [1:8763] 5.56e-87 1.57e-129 3.70e-11 1.28e-147 1.72e-29 ...
  ..$ bitscore     : num [1:8763] 251 384 63.5 420 114 231 135 48.9 46.2 791 ...
 $ Aprotothecoides_Helicosporidiumsp  :'data.frame':    6491 obs. of  12 variables:
  ..$ query        : chr [1:6491] "Apro_AP00G00010" "Apro_AP00G00010" "Apro_AP00G00020" "Apro_AP00G00040" ...
  ..$ db           : chr [1:6491] "Heli_HE0000G22290" "Heli_HE0000G41900" "Heli_HE0000G22280" "Heli_HE0000G19840" ...
  ..$ perc_identity: num [1:6491] 87.4 34.7 51.9 29.8 47.4 35.8 40.3 34.2 78.4 28.6 ...
  ..$ length       : int [1:6491] 175 150 532 336 57 81 67 76 320 224 ...
  ..$ mismatches   : int [1:6491] 22 92 191 168 28 47 34 45 48 160 ...
  ..$ gap_open     : int [1:6491] 0 2 5 8 1 2 2 2 1 0 ...
  ..$ qstart       : int [1:6491] 1 27 42 42 82 86 87 90 1 50 ...
  ..$ qend         : int [1:6491] 175 170 513 361 136 163 147 160 299 273 ...
  ..$ tstart       : int [1:6491] 1 27 23 12 56 5 83 89 1 60 ...
  ..$ tend         : int [1:6491] 175 176 549 295 112 83 149 164 320 283 ...
  ..$ evalue       : num [1:6491] 1.59e-103 6.96e-18 2.53e-172 1.47e-22 2.00e-09 ...
  ..$ bitscore     : num [1:6491] 292 74.3 494 93.6 52 49.7 43.5 43.5 498 111 ...
 $ Aprotothecoides_Mpusilla           :'data.frame':    6815 obs. of  12 variables:
  ..$ query        : chr [1:6815] "Apro_AP00G00010" "Apro_AP00G00010" "Apro_AP00G00030" "Apro_AP00G00040" ...
  ..$ db           : chr [1:6815] "Mpus_MP04G06740" "Mpus_MP13G03290" "Mpus_MP06G04060" "Mpus_MP12G00580" ...
  ..$ perc_identity: num [1:6815] 80 37.9 56.3 56.7 31.7 34.3 44.3 44.1 45.1 45.5 ...
  ..$ length       : int [1:6815] 135 153 48 330 344 230 70 68 71 66 ...
  ..$ mismatches   : int [1:6815] 24 88 21 141 166 124 39 38 38 36 ...
  ..$ gap_open     : int [1:6815] 2 2 0 2 15 6 0 0 1 0 ...
  ..$ qstart       : int [1:6815] 39 24 133 30 23 10 84 87 84 81 ...
  ..$ qend         : int [1:6815] 173 169 180 359 361 212 153 154 153 146 ...
  ..$ tstart       : int [1:6815] 2 39 14 74 14 8 31 4 53 115 ...
  ..$ tend         : int [1:6815] 133 191 61 401 293 237 100 71 123 180 ...
  ..$ evalue       : num [1:6815] 2.12e-61 1.60e-22 6.98e-07 2.86e-114 1.59e-25 ...
  ..$ bitscore     : num [1:6815] 185 88.2 50.1 337 103 96.3 70.9 62.4 57.4 56.6 ...
 $ Aprotothecoides_Msp                :'data.frame':    6939 obs. of  12 variables:
  ..$ query        : chr [1:6939] "Apro_AP00G00010" "Apro_AP00G00010" "Apro_AP00G00040" "Apro_AP00G00040" ...
  ..$ db           : chr [1:6939] "Msp_MRCC299_02G03640" "Msp_MRCC299_12G05000" "Msp_MRCC299_04G00500" "Msp_MRCC299_01G05100" ...
  ..$ perc_identity: num [1:6939] 72.2 53.3 57.7 29 43.2 46.7 46.5 47.8 42.6 41.3 ...
  ..$ length       : int [1:6939] 158 152 324 345 148 75 71 69 68 75 ...
  ..$ mismatches   : int [1:6939] 41 69 134 181 61 38 35 35 39 42 ...
  ..$ gap_open     : int [1:6939] 1 1 2 12 4 1 1 1 0 1 ...
  ..$ qstart       : int [1:6939] 16 18 36 21 1 86 87 87 87 86 ...
  ..$ qend         : int [1:6939] 173 169 359 361 127 158 154 154 154 158 ...
  ..$ tstart       : int [1:6939] 23 5 2 36 1 5 31 29 4 10 ...
  ..$ tend         : int [1:6939] 177 154 322 320 146 79 101 97 71 84 ...
  ..$ evalue       : num [1:6939] 2.81e-70 1.47e-46 1.57e-119 4.98e-23 1.16e-23 ...
  ..$ bitscore     : num [1:6939] 209 148 347 96.7 98.6 64.7 62.4 61.6 59.7 58.2 ...
 $ Aprotothecoides_Olucimarinus       :'data.frame':    6361 obs. of  12 variables:
  ..$ query        : chr [1:6361] "Apro_AP00G00010" "Apro_AP00G00010" "Apro_AP00G00010" "Apro_AP00G00010" ...
  ..$ db           : chr [1:6361] "Oluc_OL07G02270" "Oluc_OL02G03300" "Oluc_OL02G03310" "Oluc_OL01G03000" ...
  ..$ perc_identity: num [1:6361] 77.1 48.3 47.9 39.6 36.6 62.6 29.3 37.1 40 45.9 ...
  ..$ length       : int [1:6361] 157 143 142 154 183 329 341 229 85 74 ...
  ..$ mismatches   : int [1:6361] 33 73 73 86 96 121 176 117 48 39 ...
  ..$ gap_open     : int [1:6361] 1 1 1 2 5 2 9 7 1 1 ...
  ..$ qstart       : int [1:6361] 18 24 24 24 312 31 23 9 81 82 ...
  ..$ qend         : int [1:6361] 174 166 165 170 488 359 361 213 162 154 ...
  ..$ tstart       : int [1:6361] 5 9 2 53 116 37 47 48 4 27 ...
  ..$ tend         : int [1:6361] 158 150 142 206 284 363 324 273 88 100 ...
  ..$ evalue       : num [1:6361] 1.42e-74 4.50e-38 8.99e-38 1.22e-22 9.39e-19 ...
  ..$ bitscore     : num [1:6361] 219 126 125 88.2 84.7 388 105 99 63.2 61.2 ...
 $ Aprotothecoides_Omediterraneus     :'data.frame':    6219 obs. of  12 variables:
  ..$ query        : chr [1:6219] "Apro_AP00G00010" "Apro_AP00G00010" "Apro_AP00G00010" "Apro_AP00G00020" ...
  ..$ db           : chr [1:6219] "Omed_OM_06G02480" "Omed_OM_04G01400" "Omed_OM_01G04090" "Omed_OM_02G03120" ...
  ..$ perc_identity: num [1:6219] 77.7 46.3 37.7 38 44.9 61.9 30.9 32.9 43.5 36.9 ...
  ..$ length       : int [1:6219] 157 149 154 166 49 318 337 228 69 84 ...
  ..$ mismatches   : int [1:6219] 32 77 89 78 27 119 177 130 38 51 ...
  ..$ gap_open     : int [1:6219] 2 1 1 6 0 2 13 4 1 1 ...
  ..$ qstart       : int [1:6219] 18 21 24 329 132 42 27 9 87 77 ...
  ..$ qend         : int [1:6219] 174 169 170 488 180 359 361 213 154 158 ...
  ..$ tstart       : int [1:6219] 5 4 53 144 44 1 27 50 41 1 ...
  ..$ tend         : int [1:6219] 158 149 206 290 92 316 309 277 109 84 ...
  ..$ evalue       : num [1:6219] 1.94e-73 3.52e-36 6.29e-20 6.41e-16 7.91e-06 ...
  ..$ bitscore     : num [1:6219] 216 121 81.3 76.6 46.2 371 101 82 55.8 55.5 ...
 $ Aprotothecoides_Osp                :'data.frame':    5988 obs. of  12 variables:
  ..$ query        : chr [1:5988] "Apro_AP00G00010" "Apro_AP00G00010" "Apro_AP00G00010" "Apro_AP00G00020" ...
  ..$ db           : chr [1:5988] "Osp_ORCC809_07G02470" "Osp_ORCC809_02G02230" "Osp_ORCC809_01G03740" "Osp_ORCC809_04G02330" ...
  ..$ perc_identity: num [1:5988] 75.5 49 39.6 38.1 62 29.2 34.2 47.1 40.5 44.9 ...
  ..$ length       : int [1:5988] 159 147 154 160 329 336 225 68 74 49 ...
  ..$ mismatches   : int [1:5988] 36 72 86 85 123 176 128 35 42 25 ...
  ..$ gap_open     : int [1:5988] 1 1 2 4 2 13 5 1 1 1 ...
  ..$ qstart       : int [1:5988] 16 23 24 329 31 30 9 87 86 82 ...
  ..$ qend         : int [1:5988] 174 169 170 488 359 361 213 153 157 130 ...
  ..$ tstart       : int [1:5988] 3 9 53 141 42 47 51 2 9 287 ...
  ..$ tend         : int [1:5988] 158 152 206 286 368 324 275 69 82 333 ...
  ..$ evalue       : num [1:5988] 7.62e-75 8.43e-41 8.81e-23 2.65e-17 2.30e-134 ...
  ..$ bitscore     : num [1:5988] 219 133 88.6 80.5 386 101 92.4 57.8 57.4 45.4 ...
 $ Aprotothecoides_Otauri             :'data.frame':    6152 obs. of  12 variables:
  ..$ query        : chr [1:6152] "Apro_AP00G00010" "Apro_AP00G00010" "Apro_AP00G00010" "Apro_AP00G00020" ...
  ..$ db           : chr [1:6152] "Otau_OT_07G02030" "Otau_OT_02G01480" "Otau_OT_01G02690" "Otau_OT_04G02930" ...
  ..$ perc_identity: num [1:6152] 75.3 44.8 40.9 36.9 61.3 32 34.7 42.2 40.7 44.3 ...
  ..$ length       : int [1:6152] 158 143 154 160 318 341 222 90 86 61 ...
  ..$ mismatches   : int [1:6152] 36 78 84 87 121 167 124 48 48 32 ...
  ..$ gap_open     : int [1:6152] 1 1 2 4 2 13 6 2 1 1 ...
  ..$ qstart       : int [1:6152] 16 24 24 329 42 23 13 81 86 87 ...
  ..$ qend         : int [1:6152] 173 166 170 488 359 361 213 166 168 147 ...
  ..$ tstart       : int [1:6152] 3 9 55 141 1 34 53 30 11 13 ...
  ..$ tend         : int [1:6152] 157 150 208 286 316 311 274 119 96 71 ...
  ..$ evalue       : num [1:6152] 3.82e-75 1.49e-34 3.71e-23 3.22e-16 1.25e-129 ...
  ..$ bitscore     : num [1:6152] 220 117 89.7 77.4 372 104 89.4 61.2 57.4 55.1 ...
 $ Aprotothecoides_PicRCC4223         :'data.frame':    8299 obs. of  12 variables:
  ..$ query        : chr [1:8299] "Apro_AP00G00010" "Apro_AP00G00010" "Apro_AP00G00020" "Apro_AP00G00040" ...
  ..$ db           : chr [1:8299] "PicR_RCC4223.14g01030" "PicR_RCC4223.08g01460" "PicR_RCC4223.14g01010" "PicR_RCC4223.14g01360" ...
  ..$ perc_identity: num [1:8299] 88.3 28.8 49.5 71.3 29.3 34.7 44.9 47.4 40.9 34.4 ...
  ..$ length       : int [1:8299] 162 160 507 363 328 248 78 57 66 90 ...
  ..$ mismatches   : int [1:8299] 19 109 184 99 178 123 39 28 34 51 ...
  ..$ gap_open     : int [1:8299] 0 2 3 3 8 6 2 1 1 2 ...
  ..$ qstart       : int [1:8299] 14 15 77 1 35 1 87 82 86 64 ...
  ..$ qend         : int [1:8299] 175 169 512 361 361 212 162 136 146 147 ...
  ..$ tstart       : int [1:8299] 4 27 165 1 46 1 6 242 3 47 ...
  ..$ tend         : int [1:8299] 165 186 670 360 320 245 81 298 68 134 ...
  ..$ evalue       : num [1:8299] 1.81e-96 4.09e-13 1.19e-158 2.84e-170 4.51e-25 ...
  ..$ bitscore     : num [1:8299] 275 62.8 465 477 102 115 62.4 52 50.4 47.4 ...
 $ Aprotothecoides_PicSE3             :'data.frame':    7950 obs. of  12 variables:
  ..$ query        : chr [1:7950] "Apro_AP00G00010" "Apro_AP00G00010" "Apro_AP00G00020" "Apro_AP00G00040" ...
  ..$ db           : chr [1:7950] "PicS_PI00G08740" "PicS_PI00G51920" "PicS_PI00G08730" "PicS_PI00G08950" ...
  ..$ perc_identity: num [1:7950] 88.3 28.8 49.5 71.9 29 33.9 42.3 40.9 34.5 39.7 ...
  ..$ length       : int [1:7950] 162 160 507 363 328 251 78 66 84 68 ...
  ..$ mismatches   : int [1:7950] 19 109 184 97 179 120 41 34 47 39 ...
  ..$ gap_open     : int [1:7950] 0 2 3 3 8 8 2 1 2 2 ...
  ..$ qstart       : int [1:7950] 14 15 77 1 35 1 87 86 70 90 ...
  ..$ qend         : int [1:7950] 175 169 512 361 361 212 162 146 147 155 ...
  ..$ tstart       : int [1:7950] 4 27 168 1 46 1 6 3 98 106 ...
  ..$ tend         : int [1:7950] 165 186 673 360 320 244 81 68 179 173 ...
  ..$ evalue       : num [1:7950] 1.53e-96 1.78e-13 1.25e-157 5.90e-171 7.20e-25 ...
  ..$ bitscore     : num [1:7950] 275 63.5 462 478 101 107 58.9 49.7 45.8 45.4 ...
 $ Aprotothecoides_Ppatens            :'data.frame':    11217 obs. of  12 variables:
  ..$ query        : chr [1:11217] "Apro_AP00G00010" "Apro_AP00G00010" "Apro_AP00G00010" "Apro_AP00G00010" ...
  ..$ db           : chr [1:11217] "Ppat_PP00045G00600" "Ppat_PP00001G00160" "Ppat_PP00002G00570" "Ppat_PP00045G00580" ...
  ..$ perc_identity: num [1:11217] 80.4 79.8 79.8 79.8 79.8 30.5 31 59.1 59 58.5 ...
  ..$ length       : int [1:11217] 163 163 163 163 163 449 461 323 322 323 ...
  ..$ mismatches   : int [1:11217] 31 32 32 32 32 260 259 129 129 131 ...
  ..$ gap_open     : int [1:11217] 1 1 1 1 1 10 13 2 2 2 ...
  ..$ qstart       : int [1:11217] 9 9 9 9 9 86 66 37 37 37 ...
  ..$ qend         : int [1:11217] 171 171 171 171 171 511 493 359 358 359 ...
  ..$ tstart       : int [1:11217] 1 1 1 1 1 57 25 56 56 56 ...
  ..$ tend         : int [1:11217] 162 162 162 162 162 476 459 375 374 375 ...
  ..$ evalue       : num [1:11217] 4.96e-83 2.02e-82 2.02e-82 2.02e-82 2.02e-82 ...
  ..$ bitscore     : num [1:11217] 242 240 240 240 240 182 160 357 357 355 ...
 $ Aprotothecoides_Vcarteri           :'data.frame':    7995 obs. of  12 variables:
  ..$ query        : chr [1:7995] "Apro_AP00G00010" "Apro_AP00G00020" "Apro_AP00G00020" "Apro_AP00G00020" ...
  ..$ db           : chr [1:7995] "Vcar_VC00G73820" "Vcar_VC00G97140" "Vcar_VC00G16690" "Vcar_VC00G97670" ...
  ..$ perc_identity: num [1:7995] 70.4 33.7 51.2 37.4 52.1 61.8 33.9 39 43.7 43.8 ...
  ..$ length       : int [1:7995] 169 543 217 238 48 335 342 236 71 80 ...
  ..$ mismatches   : int [1:7995] 47 250 97 99 23 124 153 115 38 41 ...
  ..$ gap_open     : int [1:7995] 1 6 2 4 0 3 13 4 1 2 ...
  ..$ qstart       : int [1:7995] 5 77 305 325 133 25 34 3 87 70 ...
  ..$ qend         : int [1:7995] 173 510 512 512 180 359 361 211 155 146 ...
  ..$ tstart       : int [1:7995] 5 127 389 481 40 26 42 2 6 385 ...
  ..$ tend         : int [1:7995] 170 668 605 718 87 356 324 235 76 463 ...
  ..$ evalue       : num [1:7995] 3.71e-70 3.26e-85 5.27e-59 1.66e-31 4.71e-09 ...
  ..$ bitscore     : num [1:7995] 209 276 205 128 57.8 382 110 139 57.8 54.7 ...
 $ Asterochlorissp_Aprotothecoides    :'data.frame':    9975 obs. of  12 variables:
  ..$ query        : chr [1:9975] "Aste_AC00G00020" "Aste_AC00G00030" "Aste_AC00G00040" "Aste_AC00G00090" ...
  ..$ db           : chr [1:9975] "Apro_AP00G33190" "Apro_AP00G31270" "Apro_AP00G64170" "Apro_AP00G15010" ...
  ..$ perc_identity: num [1:9975] 27.7 42 75.9 62.2 48.1 65.8 48.8 37.9 65.9 58.1 ...
  ..$ length       : int [1:9975] 462 176 274 270 501 400 418 132 314 322 ...
  ..$ mismatches   : int [1:9975] 254 90 63 102 246 103 171 67 104 116 ...
  ..$ gap_open     : int [1:9975] 12 2 2 0 5 4 8 5 1 3 ...
  ..$ qstart       : int [1:9975] 20 30 1 1 26 2 9 121 69 71 ...
  ..$ qend         : int [1:9975] 442 200 274 270 523 399 389 238 379 382 ...
  ..$ tstart       : int [1:9975] 622 40 25 45 27 69 24 222 34 73 ...
  ..$ tend         : int [1:9975] 1042 208 295 314 516 436 435 352 347 385 ...
  ..$ evalue       : num [1:9975] 3.14e-24 2.44e-39 1.78e-149 7.94e-132 9.39e-142 ...
  ..$ bitscore     : num [1:9975] 103 132 422 374 428 531 384 76.6 397 341 ...
 $ Asterochlorissp_Asterochlorissp    :'data.frame':    20581 obs. of  12 variables:
  ..$ query        : chr [1:20581] "Aste_AC00G00010" "Aste_AC00G00010" "Aste_AC00G00020" "Aste_AC00G00020" ...
  ..$ db           : chr [1:20581] "Aste_AC00G00010" "Aste_AC00G80100" "Aste_AC00G00020" "Aste_AC00G80120" ...
  ..$ perc_identity: num [1:20581] 100 43.8 100 78.7 41.2 45.7 35.1 100 100 100 ...
  ..$ length       : int [1:20581] 280 201 450 450 165 105 188 213 342 72 ...
  ..$ mismatches   : int [1:20581] 0 110 0 50 82 57 103 0 0 0 ...
  ..$ gap_open     : int [1:20581] 0 2 0 2 3 0 3 0 0 0 ...
  ..$ qstart       : int [1:20581] 1 51 1 1 25 85 25 1 1 1 ...
  ..$ qend         : int [1:20581] 280 251 450 450 189 189 207 213 342 72 ...
  ..$ tstart       : int [1:20581] 1 2 1 1 62 6 76 1 1 1 ...
  ..$ tend         : int [1:20581] 280 199 450 404 211 110 249 213 342 72 ...
  ..$ evalue       : num [1:20581] 1.30e-212 4.25e-50 0.00 2.62e-252 2.23e-22 ...
  ..$ bitscore     : num [1:20581] 577 162 908 690 98.2 83.6 87 421 631 147 ...
 $ Asterochlorissp_Bprasinos          :'data.frame':    7974 obs. of  12 variables:
  ..$ query        : chr [1:7974] "Aste_AC00G00020" "Aste_AC00G00020" "Aste_AC00G00020" "Aste_AC00G00040" ...
  ..$ db           : chr [1:7974] "Bpra_BPRRCC1105_13G01010" "Bpra_BPRRCC1105_06G01160" "Bpra_BPRRCC1105_05G02330" "Bpra_BPRRCC1105_15G00750" ...
  ..$ perc_identity: num [1:7974] 31 43 25.1 68.9 51.2 37.6 58.5 39.2 48.9 39.6 ...
  ..$ length       : int [1:7974] 468 100 463 302 41 109 436 441 262 240 ...
  ..$ mismatches   : int [1:7974] 238 57 271 92 20 68 141 181 103 128 ...
  ..$ gap_open     : int [1:7974] 14 0 14 1 0 0 5 8 5 6 ...
  ..$ qstart       : int [1:7974] 27 85 27 1 5 28 3 42 119 18 ...
  ..$ qend         : int [1:7974] 442 184 445 302 45 136 400 395 350 247 ...
  ..$ tstart       : int [1:7974] 70 182 118 25 244 3 27 156 433 29 ...
  ..$ tend         : int [1:7974] 504 281 548 324 284 111 460 596 693 261 ...
  ..$ evalue       : num [1:7974] 8.08e-46 3.19e-17 3.07e-15 3.12e-153 7.89e-07 ...
  ..$ bitscore     : num [1:7974] 167 82.4 76.6 434 42.7 80.1 498 298 238 155 ...
 $ Asterochlorissp_Chlorellasp        :'data.frame':    11967 obs. of  12 variables:
  ..$ query        : chr [1:11967] "Aste_AC00G00020" "Aste_AC00G00020" "Aste_AC00G00020" "Aste_AC00G00020" ...
  ..$ db           : chr [1:11967] "Chlo_CNC64A_013G02700" "Chlo_CNC64A_010G01270" "Chlo_CNC64A_026G00430" "Chlo_CNC64A_010G00750" ...
  ..$ perc_identity: num [1:11967] 46.6 42.9 37.1 36.6 78.5 45 69.3 35.3 53.9 42.5 ...
  ..$ length       : int [1:11967] 429 429 194 205 274 60 238 252 514 146 ...
  ..$ mismatches   : int [1:11967] 182 178 108 113 52 33 73 107 221 82 ...
  ..$ gap_open     : int [1:11967] 4 9 2 3 1 0 0 4 6 2 ...
  ..$ qstart       : int [1:11967] 21 25 20 6 1 4 5 21 18 10 ...
  ..$ qend         : int [1:11967] 449 445 213 208 274 63 242 243 523 155 ...
  ..$ tstart       : int [1:11967] 67 1 75 46 28 833 1 14 26 13 ...
  ..$ tend         : int [1:11967] 448 370 254 235 294 892 238 238 531 156 ...
  ..$ evalue       : num [1:11967] 4.76e-122 2.82e-89 6.38e-23 2.79e-22 3.44e-156 ...
  ..$ bitscore     : num [1:11967] 361 275 99.8 97.8 443 48.1 362 108 522 113 ...
 $ Asterochlorissp_Creinhardtii       :'data.frame':    13098 obs. of  12 variables:
  ..$ query        : chr [1:13098] "Aste_AC00G00020" "Aste_AC00G00020" "Aste_AC00G00020" "Aste_AC00G00030" ...
  ..$ db           : chr [1:13098] "Crei_CR11G01060" "Crei_CR10G04730" "Crei_CR08G01050" "Crei_CR01G04360" ...
  ..$ perc_identity: num [1:13098] 44.3 29.6 39.1 43.9 78.1 42.4 61.3 36.9 37.4 35.1 ...
  ..$ length       : int [1:13098] 506 446 161 180 283 59 274 561 516 516 ...
  ..$ mismatches   : int [1:13098] 171 253 82 91 51 34 106 286 301 315 ...
  ..$ gap_open     : int [1:13098] 5 14 3 5 2 0 0 6 8 8 ...
  ..$ qstart       : int [1:13098] 9 21 22 29 1 5 1 26 26 17 ...
  ..$ qend         : int [1:13098] 449 437 181 200 274 63 274 523 527 523 ...
  ..$ tstart       : int [1:13098] 65 94 62 41 26 1752 82 30 102 111 ...
  ..$ tend         : int [1:13098] 524 507 207 218 306 1810 355 585 609 615 ...
  ..$ evalue       : num [1:13098] 3.66e-125 6.34e-22 1.22e-17 1.72e-37 1.04e-158 ...
  ..$ bitscore     : num [1:13098] 374 98.2 85.1 129 451 41.6 370 327 312 280 ...
 $ Asterochlorissp_Csubellipsoidea    :'data.frame':    13255 obs. of  12 variables:
  ..$ query        : chr [1:13255] "Aste_AC00G00010" "Aste_AC00G00010" "Aste_AC00G00020" "Aste_AC00G00020" ...
  ..$ db           : chr [1:13255] "Csub_CV00G14160" "Csub_CV00G29290" "Csub_CV00G29500" "Csub_CV00G93540" ...
  ..$ perc_identity: num [1:13255] 54.5 38.8 51.9 42.3 37.4 26.5 74.3 63.2 59.1 70 ...
  ..$ length       : int [1:13255] 253 263 437 168 182 446 304 38 66 277 ...
  ..$ mismatches   : int [1:13255] 115 149 152 82 99 271 75 14 27 83 ...
  ..$ gap_open     : int [1:13255] 0 5 6 2 3 14 2 0 0 0 ...
  ..$ qstart       : int [1:13255] 27 16 21 22 9 21 1 4 15 1 ...
  ..$ qend         : int [1:13255] 279 269 450 189 189 449 304 41 80 277 ...
  ..$ tstart       : int [1:13255] 11 4 18 61 141 72 25 143 12 11 ...
  ..$ tend         : int [1:13255] 263 263 403 213 308 477 325 180 77 287 ...
  ..$ evalue       : num [1:13255] 1.21e-95 4.62e-49 4.68e-140 6.76e-26 5.67e-22 ...
  ..$ bitscore     : num [1:13255] 281 162 405 108 97.1 89 455 45.1 84.3 434 ...
 $ Asterochlorissp_Helicosporidiumsp  :'data.frame':    6839 obs. of  12 variables:
  ..$ query        : chr [1:6839] "Aste_AC00G00040" "Aste_AC00G00050" "Aste_AC00G00120" "Aste_AC00G00130" ...
  ..$ db           : chr [1:6839] "Heli_HE0000G21900" "Heli_HE0000G49670" "Heli_HE0000G05790" "Heli_HE0000G45940" ...
  ..$ perc_identity: num [1:6839] 73.4 68 46 37.8 63.8 52.5 56.2 51.4 64.3 40.3 ...
  ..$ length       : int [1:6839] 274 25 509 127 401 301 313 259 157 144 ...
  ..$ mismatches   : int [1:6839] 71 8 261 79 130 121 134 123 52 76 ...
  ..$ gap_open     : int [1:6839] 1 0 6 0 5 3 2 2 1 4 ...
  ..$ qstart       : int [1:6839] 1 5 18 16 1 111 69 121 54 1 ...
  ..$ qend         : int [1:6839] 274 29 523 142 394 389 378 376 206 142 ...
  ..$ tstart       : int [1:6839] 23 212 20 19 24 51 73 19 2 14 ...
  ..$ tend         : int [1:6839] 294 236 517 145 416 351 385 277 158 149 ...
  ..$ evalue       : num [1:6839] 9.08e-149 9.84e-06 1.90e-138 5.70e-28 2.75e-187 ...
  ..$ bitscore     : num [1:6839] 421 38.5 411 98.6 523 337 328 251 192 83.6 ...
 $ Asterochlorissp_Mpusilla           :'data.frame':    9547 obs. of  12 variables:
  ..$ query        : chr [1:9547] "Aste_AC00G00010" "Aste_AC00G00020" "Aste_AC00G00020" "Aste_AC00G00020" ...
  ..$ db           : chr [1:9547] "Mpus_MP13G03450" "Mpus_MP06G00320" "Mpus_MP10G03710" "Mpus_MP02G02950" ...
  ..$ perc_identity: num [1:9547] 32.6 37 35.2 34.8 32.2 72.8 44.3 44.1 61.9 42.7 ...
  ..$ length       : int [1:9547] 175 487 435 184 143 265 61 127 407 424 ...
  ..$ mismatches   : int [1:9547] 103 228 226 105 54 70 34 71 128 167 ...
  ..$ gap_open     : int [1:9547] 4 10 10 3 2 1 0 0 6 8 ...
  ..$ qstart       : int [1:9547] 62 20 27 1 85 7 5 16 3 19 ...
  ..$ qend         : int [1:9547] 221 449 442 184 188 271 65 142 400 366 ...
  ..$ tstart       : int [1:9547] 34 49 85 89 131 83 267 20 59 6 ...
  ..$ tend         : int [1:9547] 208 513 482 257 269 345 327 146 447 429 ...
  ..$ evalue       : num [1:9547] 2.32e-18 2.20e-74 3.78e-64 9.00e-20 2.78e-11 ...
  ..$ bitscore     : num [1:9547] 83.2 241 217 90.5 64.3 404 47.8 108 505 316 ...
 $ Asterochlorissp_Msp                :'data.frame':    9692 obs. of  12 variables:
  ..$ query        : chr [1:9692] "Aste_AC00G00020" "Aste_AC00G00020" "Aste_AC00G00020" "Aste_AC00G00020" ...
  ..$ db           : chr [1:9692] "Msp_MRCC299_03G00340" "Msp_MRCC299_12G01280" "Msp_MRCC299_01G06690" "Msp_MRCC299_02G08570" ...
  ..$ perc_identity: num [1:9692] 41.9 31.5 26.1 30.2 67.2 42.4 55.9 44.1 63.4 46.2 ...
  ..$ length       : int [1:9692] 427 429 460 463 302 59 68 118 407 409 ...
  ..$ mismatches   : int [1:9692] 190 254 247 241 97 34 30 66 123 177 ...
  ..$ gap_open     : int [1:9692] 7 9 18 20 1 0 0 0 6 9 ...
  ..$ qstart       : int [1:9692] 24 18 21 27 1 5 8 19 3 9 ...
  ..$ qend         : int [1:9692] 438 442 442 442 302 63 75 136 400 374 ...
  ..$ tstart       : int [1:9692] 4 47 108 19 28 90 14 25 56 70 ...
  ..$ tend         : int [1:9692] 384 439 512 446 327 148 81 142 445 478 ...
  ..$ evalue       : num [1:9692] 1.16e-92 8.36e-58 1.89e-19 1.45e-18 8.74e-149 ...
  ..$ bitscore     : num [1:9692] 284 198 89.4 86.3 423 44.7 77.4 97.8 518 340 ...
 $ Asterochlorissp_Olucimarinus       :'data.frame':    8599 obs. of  12 variables:
  ..$ query        : chr [1:8599] "Aste_AC00G00020" "Aste_AC00G00020" "Aste_AC00G00020" "Aste_AC00G00020" ...
  ..$ db           : chr [1:8599] "Oluc_OL11G02410" "Oluc_OL06G02190" "Oluc_OL02G04130" "Oluc_OL02G04140" ...
  ..$ perc_identity: num [1:8599] 35.4 25.3 41 41 67 44.6 41.2 63.8 46.5 50.4 ...
  ..$ length       : int [1:8599] 438 474 100 100 306 56 97 392 398 254 ...
  ..$ mismatches   : int [1:8599] 222 284 59 59 98 31 57 126 191 107 ...
  ..$ gap_open     : int [1:8599] 11 16 0 0 2 0 0 4 8 5 ...
  ..$ qstart       : int [1:8599] 26 14 85 85 1 5 19 5 7 120 ...
  ..$ qend         : int [1:8599] 450 445 184 184 306 60 115 393 387 355 ...
  ..$ tstart       : int [1:8599] 39 92 163 163 43 103 20 30 21 140 ...
  ..$ tend         : int [1:8599] 428 537 262 262 345 158 116 408 413 392 ...
  ..$ evalue       : num [1:8599] 4.14e-65 9.45e-19 4.02e-16 4.02e-16 6.19e-145 ...
  ..$ bitscore     : num [1:8599] 217 86.7 78.6 78.6 414 38.9 87 507 343 240 ...
 $ Asterochlorissp_Omediterraneus     :'data.frame':    8446 obs. of  12 variables:
  ..$ query        : chr [1:8446] "Aste_AC00G00020" "Aste_AC00G00020" "Aste_AC00G00020" "Aste_AC00G00020" ...
  ..$ db           : chr [1:8446] "Omed_OM_11G02600" "Omed_OM_05G00440" "Omed_OM_05G02200" "Omed_OM_04G01120" ...
  ..$ perc_identity: num [1:8446] 36.9 35.5 26.3 38.1 64.9 38.1 62.8 45 47.8 44.3 ...
  ..$ length       : int [1:8446] 442 439 482 105 302 126 400 411 289 237 ...
  ..$ mismatches   : int [1:8446] 216 231 254 62 103 78 132 194 133 117 ...
  ..$ gap_open     : int [1:8446] 12 10 13 1 2 0 4 7 4 5 ...
  ..$ qstart       : int [1:8446] 21 25 21 94 1 19 5 10 118 14 ...
  ..$ qend         : int [1:8446] 445 445 447 195 302 144 400 388 389 241 ...
  ..$ tstart       : int [1:8446] 63 117 32 1 44 22 61 32 202 73 ...
  ..$ tend         : int [1:8446] 458 521 467 105 342 147 447 442 489 303 ...
  ..$ evalue       : num [1:8446] 3.98e-71 1.82e-65 2.07e-25 8.38e-14 4.27e-137 ...
  ..$ bitscore     : num [1:8446] 234 217 107 70.9 394 91.3 513 342 264 176 ...
 $ Asterochlorissp_Osp                :'data.frame':    8188 obs. of  12 variables:
  ..$ query        : chr [1:8188] "Aste_AC00G00020" "Aste_AC00G00020" "Aste_AC00G00020" "Aste_AC00G00040" ...
  ..$ db           : chr [1:8188] "Osp_ORCC809_06G00410" "Osp_ORCC809_11G03280" "Osp_ORCC809_06G02060" "Osp_ORCC809_07G04730" ...
  ..$ perc_identity: num [1:8188] 38.5 37.1 28.4 66.3 40.3 36.7 64.5 46 43.8 61.4 ...
  ..$ length       : int [1:8188] 447 442 469 306 62 128 392 385 283 316 ...
  ..$ mismatches   : int [1:8188] 221 229 260 100 37 79 123 170 137 122 ...
  ..$ gap_open     : int [1:8188] 11 13 19 2 0 1 4 7 5 0 ...
  ..$ qstart       : int [1:8188] 19 18 21 1 4 20 5 42 125 65 ...
  ..$ qend         : int [1:8188] 445 450 441 306 65 147 393 388 386 380 ...
  ..$ tstart       : int [1:8188] 27 63 71 38 123 548 30 71 1 2 ...
  ..$ tend         : int [1:8188] 439 464 511 340 184 673 408 455 282 317 ...
  ..$ evalue       : num [1:8188] 2.78e-77 1.44e-68 1.92e-23 1.66e-144 2.44e-06 ...
  ..$ bitscore     : num [1:8188] 246 227 101 411 40.8 86.7 514 325 233 387 ...
 $ Asterochlorissp_Otauri             :'data.frame':    8322 obs. of  12 variables:
  ..$ query        : chr [1:8322] "Aste_AC00G00020" "Aste_AC00G00020" "Aste_AC00G00020" "Aste_AC00G00020" ...
  ..$ db           : chr [1:8322] "Otau_OT_06G00510" "Otau_OT_11G02420" "Otau_OT_06G02220" "Otau_OT_02G00870" ...
  ..$ perc_identity: num [1:8322] 38.7 35.5 27.9 43.9 67.3 41 35 64.6 43.1 44.7 ...
  ..$ length       : int [1:8322] 445 440 466 98 306 61 120 395 415 302 ...
  ..$ mismatches   : int [1:8322] 219 240 259 53 97 36 78 123 201 141 ...
  ..$ gap_open     : int [1:8322] 10 11 18 2 2 0 0 5 8 6 ...
  ..$ qstart       : int [1:8322] 21 19 22 88 1 5 18 3 9 113 ...
  ..$ qend         : int [1:8322] 445 450 445 184 306 65 137 393 388 391 ...
  ..$ tstart       : int [1:8322] 28 61 53 141 44 118 21 29 21 102 ...
  ..$ tend         : int [1:8322] 438 464 483 237 346 178 140 410 435 400 ...
  ..$ evalue       : num [1:8322] 5.00e-79 9.36e-65 2.67e-25 3.16e-15 1.13e-144 ...
  ..$ bitscore     : num [1:8322] 250 217 107 75.9 413 39.3 86.3 512 321 240 ...
 $ Asterochlorissp_PicRCC4223         :'data.frame':    10201 obs. of  12 variables:
  ..$ query        : chr [1:10201] "Aste_AC00G00020" "Aste_AC00G00030" "Aste_AC00G00040" "Aste_AC00G00100" ...
  ..$ db           : chr [1:10201] "PicR_RCC4223.01g00280" "PicR_RCC4223.05g03500" "PicR_RCC4223.05g02630" "PicR_RCC4223.05g01770" ...
  ..$ perc_identity: num [1:10201] 44.1 44.1 71.3 40.4 63.2 53.2 48.9 47.4 67.2 62.7 ...
  ..$ length       : int [1:10201] 426 177 310 109 394 389 411 228 311 311 ...
  ..$ mismatches   : int [1:10201] 190 93 87 65 133 172 176 109 97 114 ...
  ..$ gap_open     : int [1:10201] 5 2 1 0 6 4 6 4 3 1 ...
  ..$ qstart       : int [1:10201] 24 30 1 20 2 2 7 18 72 72 ...
  ..$ qend         : int [1:10201] 449 200 310 128 394 388 388 235 378 380 ...
  ..$ tstart       : int [1:10201] 72 95 20 23 56 54 40 49 64 29 ...
  ..$ tend         : int [1:10201] 449 271 327 131 438 434 445 275 373 339 ...
  ..$ evalue       : num [1:10201] 3.49e-113 3.06e-43 7.56e-157 8.24e-18 1.89e-173 ...
  ..$ bitscore     : num [1:10201] 338 144 442 84.3 489 406 390 209 397 376 ...
 $ Asterochlorissp_PicSE3             :'data.frame':    9737 obs. of  12 variables:
  ..$ query        : chr [1:9737] "Aste_AC00G00020" "Aste_AC00G00030" "Aste_AC00G00040" "Aste_AC00G00100" ...
  ..$ db           : chr [1:9737] "PicS_PI00G35540" "PicS_PI00G06080" "PicS_PI00G14400" "PicS_PI00G17610" ...
  ..$ perc_identity: num [1:9737] 44.8 45.2 79 40.4 64.7 53.5 48.4 47 65.9 62.7 ...
  ..$ length       : int [1:9737] 422 177 271 109 391 389 411 230 311 311 ...
  ..$ mismatches   : int [1:9737] 185 91 55 65 127 171 178 109 101 114 ...
  ..$ gap_open     : int [1:9737] 5 2 1 0 5 4 6 4 3 1 ...
  ..$ qstart       : int [1:9737] 24 30 1 20 5 2 7 18 72 72 ...
  ..$ qend         : int [1:9737] 445 200 271 128 394 388 388 235 378 380 ...
  ..$ tstart       : int [1:9737] 28 95 20 23 59 52 38 60 65 29 ...
  ..$ tend         : int [1:9737] 401 271 288 131 439 432 443 288 374 339 ...
  ..$ evalue       : num [1:9737] 1.83e-116 1.60e-44 1.15e-156 9.10e-18 5.65e-179 ...
  ..$ bitscore     : num [1:9737] 345 147 441 84 503 407 384 212 392 377 ...
 $ Asterochlorissp_Ppatens            :'data.frame':    15886 obs. of  12 variables:
  ..$ query        : chr [1:15886] "Aste_AC00G00020" "Aste_AC00G00020" "Aste_AC00G00020" "Aste_AC00G00020" ...
  ..$ db           : chr [1:15886] "Ppat_PP00301G00220" "Ppat_PP00042G01330" "Ppat_PP00167G00260" "Ppat_PP00192G00410" ...
  ..$ perc_identity: num [1:15886] 39 36.3 37.7 48.4 28.3 49.4 67.6 56.1 62.7 34.9 ...
  ..$ length       : int [1:15886] 428 430 432 128 453 89 306 41 276 106 ...
  ..$ mismatches   : int [1:15886] 215 226 216 66 252 40 97 18 99 67 ...
  ..$ gap_open     : int [1:15886] 6 7 8 0 15 1 1 0 1 1 ...
  ..$ qstart       : int [1:15886] 26 26 26 95 20 30 1 4 1 22 ...
  ..$ qend         : int [1:15886] 446 446 446 222 439 113 306 44 272 125 ...
  ..$ tstart       : int [1:15886] 59 60 61 14 127 82 84 89 107 9 ...
  ..$ tend         : int [1:15886] 447 450 450 141 539 170 387 129 382 114 ...
  ..$ evalue       : num [1:15886] 1.76e-79 6.06e-74 7.07e-74 1.00e-26 1.34e-23 ...
  ..$ bitscore     : num [1:15886] 257 242 242 110 103 83.6 408 42.7 372 55.1 ...
 $ Asterochlorissp_Vcarteri           :'data.frame':    11701 obs. of  12 variables:
  ..$ query        : chr [1:11701] "Aste_AC00G00010" "Aste_AC00G00020" "Aste_AC00G00020" "Aste_AC00G00020" ...
  ..$ db           : chr [1:11701] "Vcar_VC00G109360" "Vcar_VC00G92830" "Vcar_VC00G92820" "Vcar_VC00G22000" ...
  ..$ perc_identity: num [1:11701] 41 44.5 47.6 28.1 38.5 69.2 61.2 37.5 29.2 37.7 ...
  ..$ length       : int [1:11701] 61 319 187 452 161 308 278 475 530 324 ...
  ..$ mismatches   : int [1:11701] 36 137 38 258 83 70 104 276 326 154 ...
  ..$ gap_open     : int [1:11701] 0 2 2 16 4 3 1 7 11 5 ...
  ..$ qstart       : int [1:11701] 83 130 19 25 22 1 1 63 28 202 ...
  ..$ qend         : int [1:11701] 143 445 185 442 181 302 274 527 523 523 ...
  ..$ tstart       : int [1:11701] 53 18 27 100 62 25 12 83 70 5 ...
  ..$ tend         : int [1:11701] 113 299 173 518 207 313 289 546 584 282 ...
  ..$ evalue       : num [1:11701] 5.77e-07 5.23e-77 7.68e-44 2.17e-22 1.80e-17 ...
  ..$ bitscore     : num [1:11701] 49.7 241 150 99 84 412 361 287 211 191 ...
 $ Bprasinos_Aprotothecoides          :'data.frame':    6033 obs. of  12 variables:
  ..$ query        : chr [1:6033] "Bpra_BPRRCC1105_00G00020" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" ...
  ..$ db           : chr [1:6033] "Apro_AP00G64160" "Apro_AP00G63530" "Apro_AP00G03490" "Apro_AP00G45800" ...
  ..$ perc_identity: num [1:6033] 30.7 29.8 34.1 29.5 27.7 32.5 30.7 37.2 45.2 46.4 ...
  ..$ length       : int [1:6033] 238 614 226 207 191 120 238 137 73 69 ...
  ..$ mismatches   : int [1:6033] 118 319 117 126 108 69 118 73 38 36 ...
  ..$ gap_open     : int [1:6033] 6 16 7 4 4 3 6 4 2 1 ...
  ..$ qstart       : int [1:6033] 229 512 878 843 889 975 229 194 207 211 ...
  ..$ qend         : int [1:6033] 461 1049 1093 1049 1053 1083 461 323 279 279 ...
  ..$ tstart       : int [1:6033] 105 259 397 559 667 778 105 470 766 678 ...
  ..$ tend         : int [1:6033] 300 836 600 745 853 896 300 600 836 745 ...
  ..$ evalue       : num [1:6033] 1.53e-18 4.08e-49 2.45e-18 1.34e-15 9.42e-12 ...
  ..$ bitscore     : num [1:6033] 85.1 187 88.2 79.7 67.4 53.1 85.1 62.8 57.4 56.6 ...
 $ Bprasinos_Asterochlorissp          :'data.frame':    7217 obs. of  12 variables:
  ..$ query        : chr [1:7217] "Bpra_BPRRCC1105_00G00020" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" ...
  ..$ db           : chr [1:7217] "Aste_AC00G16670" "Aste_AC00G70120" "Aste_AC00G24240" "Aste_AC00G51400" ...
  ..$ perc_identity: num [1:7217] 34.9 29.9 31.4 28.1 29.6 24.2 34.9 45.5 40.5 36.1 ...
  ..$ length       : int [1:7217] 209 585 567 242 179 496 209 77 79 72 ...
  ..$ mismatches   : int [1:7217] 99 351 311 146 111 301 99 40 46 46 ...
  ..$ gap_open     : int [1:7217] 3 10 15 8 4 14 3 2 1 0 ...
  ..$ qstart       : int [1:7217] 253 505 518 834 889 593 253 203 208 212 ...
  ..$ qend         : int [1:7217] 461 1056 1049 1053 1053 1036 461 279 286 283 ...
  ..$ tstart       : int [1:7217] 165 336 204 524 562 278 165 653 817 688 ...
  ..$ tend         : int [1:7217] 336 894 727 759 739 750 336 727 894 759 ...
  ..$ evalue       : num [1:7217] 1.80e-29 1.49e-53 8.00e-53 7.58e-13 2.56e-11 ...
  ..$ bitscore     : num [1:7217] 118 202 198 71.6 66.6 54.3 118 58.9 53.5 51.6 ...
 $ Bprasinos_Bprasinos                :'data.frame':    13356 obs. of  12 variables:
  ..$ query        : chr [1:13356] "Bpra_BPRRCC1105_00G00010" "Bpra_BPRRCC1105_00G00010" "Bpra_BPRRCC1105_00G00010" "Bpra_BPRRCC1105_00G00010" ...
  ..$ db           : chr [1:13356] "Bpra_BPRRCC1105_00G00010" "Bpra_BPRRCC1105_11G03470" "Bpra_BPRRCC1105_00G00080" "Bpra_BPRRCC1105_11G03450" ...
  ..$ perc_identity: num [1:13356] 100 100 100 100 100 100 100 100 100 99.8 ...
  ..$ length       : int [1:13356] 229 120 120 120 120 464 464 464 461 461 ...
  ..$ mismatches   : int [1:13356] 0 0 0 0 0 0 0 0 0 1 ...
  ..$ gap_open     : int [1:13356] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ qstart       : int [1:13356] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ qend         : int [1:13356] 229 120 120 120 120 464 464 464 461 461 ...
  ..$ tstart       : int [1:13356] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ tend         : int [1:13356] 229 120 120 120 120 464 464 464 461 461 ...
  ..$ evalue       : num [1:13356] 8.67e-81 7.47e-50 1.61e-49 1.73e-49 1.73e-49 ...
  ..$ bitscore     : num [1:13356] 239 171 171 171 171 801 801 801 794 792 ...
 $ Bprasinos_Chlorellasp              :'data.frame':    6958 obs. of  12 variables:
  ..$ query        : chr [1:6958] "Bpra_BPRRCC1105_00G00020" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" ...
  ..$ db           : chr [1:6958] "Chlo_CNC64A_014G03270" "Chlo_CNC64A_003G05350" "Chlo_CNC64A_004G04660" "Chlo_CNC64A_014G01100" ...
  ..$ perc_identity: num [1:6958] 30.9 33.4 31.7 25.4 31.1 23.1 30.9 50 47.6 41.1 ...
  ..$ length       : int [1:6958] 288 560 520 441 238 605 288 112 82 107 ...
  ..$ mismatches   : int [1:6958] 131 263 292 218 114 374 131 56 41 62 ...
  ..$ gap_open     : int [1:6958] 7 11 14 9 5 17 7 0 2 1 ...
  ..$ qstart       : int [1:6958] 187 535 564 702 890 517 187 208 203 213 ...
  ..$ qend         : int [1:6958] 461 1089 1054 1056 1088 1060 461 319 284 318 ...
  ..$ tstart       : int [1:6958] 130 119 278 572 518 83 130 462 684 638 ...
  ..$ tend         : int [1:6958] 362 573 763 987 744 657 362 573 763 744 ...
  ..$ evalue       : num [1:6958] 7.67e-25 2.05e-59 1.09e-49 2.77e-18 4.86e-15 ...
  ..$ bitscore     : num [1:6958] 105 218 188 89.4 78.6 77.8 105 98.6 65.5 61.6 ...
 $ Bprasinos_Creinhardtii             :'data.frame':    7712 obs. of  12 variables:
  ..$ query        : chr [1:7712] "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" ...
  ..$ db           : chr [1:7712] "Crei_CR16G05850" "Crei_CR10G01100" "Crei_CR10G01650" "Crei_CR17G05420" ...
  ..$ perc_identity: num [1:7712] 28.4 28.6 35.9 29.4 25 46.8 44.6 44.6 47.1 53.1 ...
  ..$ length       : int [1:7712] 694 548 315 313 553 77 74 74 70 64 ...
  ..$ mismatches   : int [1:7712] 319 303 181 178 348 39 41 41 36 29 ...
  ..$ gap_open     : int [1:7712] 14 13 7 5 16 2 0 0 1 1 ...
  ..$ qstart       : int [1:7712] 511 564 512 494 535 203 210 210 210 211 ...
  ..$ qend         : int [1:7712] 1049 1049 810 767 1044 279 283 283 279 274 ...
  ..$ tstart       : int [1:7712] 411 434 345 242 105 881 811 800 1013 1443 ...
  ..$ tend         : int [1:7712] 1081 955 654 550 633 955 884 873 1081 1505 ...
  ..$ evalue       : num [1:7712] 7.84e-52 2.06e-37 1.30e-34 1.17e-25 4.43e-13 ...
  ..$ bitscore     : num [1:7712] 199 152 144 115 73.9 62.8 60.1 59.7 57.4 55.5 ...
 $ Bprasinos_Csubellipsoidea          :'data.frame':    7249 obs. of  12 variables:
  ..$ query        : chr [1:7249] "Bpra_BPRRCC1105_00G00020" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" ...
  ..$ db           : chr [1:7249] "Csub_CV00G91650" "Csub_CV00G19250" "Csub_CV00G24640" "Csub_CV00G45000" ...
  ..$ perc_identity: num [1:7249] 26.3 43.5 33.5 33.4 29.7 30.1 26.3 58.6 43 45.6 ...
  ..$ length       : int [1:7249] 441 630 609 515 633 559 441 111 100 79 ...
  ..$ mismatches   : int [1:7249] 236 317 320 285 349 326 236 46 55 42 ...
  ..$ gap_open     : int [1:7249] 9 11 15 11 14 14 9 0 2 1 ...
  ..$ qstart       : int [1:7249] 22 468 512 564 511 512 22 209 211 206 ...
  ..$ qend         : int [1:7249] 461 1089 1079 1054 1085 1044 461 319 309 284 ...
  ..$ tstart       : int [1:7249] 3 1 293 279 329 381 3 489 759 682 ...
  ..$ tend         : int [1:7249] 355 599 857 759 923 900 355 599 857 759 ...
  ..$ evalue       : num [1:7249] 3.29e-36 1.33e-124 1.49e-59 2.29e-57 7.90e-57 ...
  ..$ bitscore     : num [1:7249] 137 394 219 212 212 198 137 108 64.7 63.2 ...
 $ Bprasinos_Helicosporidiumsp        :'data.frame':    4288 obs. of  12 variables:
  ..$ query        : chr [1:4288] "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00050" "Bpra_BPRRCC1105_01G00010" "Bpra_BPRRCC1105_01G00050" ...
  ..$ db           : chr [1:4288] "Heli_HE0000G57550" "Heli_HE0000G57550" "Heli_HE0000G45320" "Heli_HE0000G41000" ...
  ..$ perc_identity: num [1:4288] 51.8 51.8 39.2 50.2 45.8 74.5 74.3 49.6 44.4 38.5 ...
  ..$ length       : int [1:4288] 56 56 125 215 491 687 35 683 707 714 ...
  ..$ mismatches   : int [1:4288] 25 25 66 104 210 167 9 321 361 372 ...
  ..$ gap_open     : int [1:4288] 2 2 2 2 8 3 0 10 15 13 ...
  ..$ qstart       : int [1:4288] 972 202 62 984 76 26 1 105 99 107 ...
  ..$ qend         : int [1:4288] 1027 257 177 1196 551 712 35 782 801 778 ...
  ..$ tstart       : int [1:4288] 417 417 11 79 61 48 1 80 4 31 ...
  ..$ tend         : int [1:4288] 470 470 134 292 510 726 35 744 682 719 ...
  ..$ evalue       : num [1:4288] 3.25e-06 7.59e-07 7.91e-20 1.43e-61 2.82e-132 ...
  ..$ bitscore     : num [1:4288] 48.1 48.1 80.5 210 393 ...
 $ Bprasinos_Mpusilla                 :'data.frame':    9152 obs. of  12 variables:
  ..$ query        : chr [1:9152] "Bpra_BPRRCC1105_00G00020" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" ...
  ..$ db           : chr [1:9152] "Mpus_MP01G07040" "Mpus_MP01G07830" "Mpus_MP06G03990" "Mpus_MP10G03780" ...
  ..$ perc_identity: num [1:9152] 33.1 55.2 26.8 29.9 27.9 28.8 33.1 60.5 38.3 38.8 ...
  ..$ length       : int [1:9152] 480 768 828 592 639 593 480 152 133 80 ...
  ..$ mismatches   : int [1:9152] 242 333 515 331 331 346 242 59 73 49 ...
  ..$ gap_open     : int [1:9152] 17 6 21 14 19 15 17 1 3 0 ...
  ..$ qstart       : int [1:9152] 20 332 346 512 512 511 20 175 211 211 ...
  ..$ qend         : int [1:9152] 461 1096 1107 1054 1049 1054 461 326 337 290 ...
  ..$ tstart       : int [1:9152] 3 173 35 434 489 317 3 782 868 673 ...
  ..$ tend         : int [1:9152] 441 932 837 990 1098 882 441 932 997 752 ...
  ..$ evalue       : num [1:9152] 3.83e-44 8.94e-250 5.77e-59 1.23e-51 2.85e-39 ...
  ..$ bitscore     : num [1:9152] 161 736 218 197 157 153 161 157 70.1 59.3 ...
 $ Bprasinos_Msp                      :'data.frame':    9422 obs. of  12 variables:
  ..$ query        : chr [1:9422] "Bpra_BPRRCC1105_00G00020" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" ...
  ..$ db           : chr [1:9422] "Msp_MRCC299_07G01160" "Msp_MRCC299_07G00230" "Msp_MRCC299_12G01210" "Msp_MRCC299_05G04310" ...
  ..$ perc_identity: num [1:9422] 34.3 55.2 30.6 30.6 30.2 28.4 34.3 64.8 36.8 42 ...
  ..$ length       : int [1:9422] 280 773 607 582 602 468 280 128 136 88 ...
  ..$ mismatches   : int [1:9422] 121 333 333 345 324 279 121 45 77 51 ...
  ..$ gap_open     : int [1:9422] 7 7 14 14 15 11 7 0 3 0 ...
  ..$ qstart       : int [1:9422] 190 332 512 510 511 601 190 204 211 195 ...
  ..$ qend         : int [1:9422] 461 1101 1087 1053 1054 1049 461 331 340 282 ...
  ..$ tstart       : int [1:9422] 145 11 268 377 261 2 145 646 905 796 ...
  ..$ tend         : int [1:9422] 369 773 817 937 824 432 369 773 1037 883 ...
  ..$ evalue       : num [1:9422] 4.23e-36 1.55e-259 4.96e-57 1.70e-53 8.45e-45 ...
  ..$ bitscore     : num [1:9422] 137 754 212 202 174 132 137 154 65.1 63.2 ...
 $ Bprasinos_Olucimarinus             :'data.frame':    9125 obs. of  12 variables:
  ..$ query        : chr [1:9125] "Bpra_BPRRCC1105_00G00020" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" ...
  ..$ db           : chr [1:9125] "Oluc_OL10G03200" "Oluc_OL10G03190" "Oluc_OL05G03730" "Oluc_OL11G02370" ...
  ..$ perc_identity: num [1:9125] 34 60 28.9 29.6 29.1 29.2 34 76.9 43.9 43.4 ...
  ..$ length       : int [1:9125] 467 623 781 655 653 654 467 121 114 113 ...
  ..$ mismatches   : int [1:9125] 206 239 488 376 389 389 206 28 55 55 ...
  ..$ gap_open     : int [1:9125] 12 6 20 16 16 16 12 0 3 3 ...
  ..$ qstart       : int [1:9125] 14 468 350 443 473 473 14 200 211 211 ...
  ..$ qend         : int [1:9125] 461 1090 1086 1054 1087 1088 461 320 318 317 ...
  ..$ tstart       : int [1:9125] 11 1 3 97 15 99 11 493 606 522 ...
  ..$ tend         : int [1:9125] 394 613 760 709 631 716 394 613 716 631 ...
  ..$ evalue       : num [1:9125] 1.27e-61 1.05e-223 7.95e-72 3.18e-57 3.07e-55 ...
  ..$ bitscore     : num [1:9125] 206 653 253 210 202 203 206 173 69.3 67.8 ...
 $ Bprasinos_Omediterraneus           :'data.frame':    9075 obs. of  12 variables:
  ..$ query        : chr [1:9075] "Bpra_BPRRCC1105_00G00020" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" ...
  ..$ db           : chr [1:9075] "Omed_OM_12G00410" "Omed_OM_12G00420" "Omed_OM_03G03980" "Omed_OM_11G02560" ...
  ..$ perc_identity: num [1:9075] 32.6 50.9 31.5 29.3 28.4 30 32.6 65.9 41 52.1 ...
  ..$ length       : int [1:9075] 500 907 644 629 654 574 500 123 122 73 ...
  ..$ mismatches   : int [1:9075] 210 407 389 346 391 331 210 42 62 33 ...
  ..$ gap_open     : int [1:9075] 13 11 16 17 16 12 13 0 3 2 ...
  ..$ qstart       : int [1:9075] 21 187 431 468 476 511 21 197 204 203 ...
  ..$ qend         : int [1:9075] 461 1089 1049 1045 1088 1045 461 319 318 275 ...
  ..$ tstart       : int [1:9075] 8 142 165 261 100 291 8 892 599 762 ...
  ..$ tend         : int [1:9075] 439 1014 781 841 717 832 439 1014 717 832 ...
  ..$ evalue       : num [1:9075] 7.59e-60 9.60e-266 1.15e-69 2.23e-54 2.19e-53 ...
  ..$ bitscore     : num [1:9075] 203 779 249 204 201 187 203 158 67.8 60.5 ...
 $ Bprasinos_Osp                      :'data.frame':    8812 obs. of  12 variables:
  ..$ query        : chr [1:8812] "Bpra_BPRRCC1105_00G00020" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" ...
  ..$ db           : chr [1:8812] "Osp_ORCC809_09G00410" "Osp_ORCC809_04G00090" "Osp_ORCC809_05G03640" "Osp_ORCC809_11G03240" ...
  ..$ perc_identity: num [1:8812] 34.8 50 31.8 28.9 29 31.1 34.8 65.8 38.8 57.6 ...
  ..$ length       : int [1:8812] 469 620 610 651 655 573 469 111 134 66 ...
  ..$ mismatches   : int [1:8812] 203 301 359 369 399 320 203 38 73 27 ...
  ..$ gap_open     : int [1:8812] 12 6 16 16 17 14 12 0 3 1 ...
  ..$ qstart       : int [1:8812] 14 468 510 443 468 511 14 207 191 210 ...
  ..$ qend         : int [1:8812] 461 1087 1090 1045 1088 1045 461 317 318 275 ...
  ..$ tstart       : int [1:8812] 13 1 180 97 98 302 13 501 590 773 ...
  ..$ tend         : int [1:8812] 399 611 761 701 720 837 399 611 720 837 ...
  ..$ evalue       : num [1:8812] 3.75e-63 3.69e-186 2.04e-67 1.49e-56 7.47e-52 ...
  ..$ bitscore     : num [1:8812] 211 556 241 208 196 186 211 144 68.6 62 ...
 $ Bprasinos_Otauri                   :'data.frame':    8922 obs. of  12 variables:
  ..$ query        : chr [1:8922] "Bpra_BPRRCC1105_00G00020" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" ...
  ..$ db           : chr [1:8922] "Otau_OT_02G01110" "Otau_OT_02G00890" "Otau_OT_05G03820" "Otau_OT_11G02380" ...
  ..$ perc_identity: num [1:8922] 33.8 52.1 27.3 30.7 29.2 28.9 33.8 69 39.1 50.7 ...
  ..$ length       : int [1:8922] 474 907 807 662 648 578 474 126 115 69 ...
  ..$ mismatches   : int [1:8922] 220 384 514 362 392 333 220 39 60 33 ...
  ..$ gap_open     : int [1:8922] 13 12 18 19 17 14 13 0 3 1 ...
  ..$ qstart       : int [1:8922] 18 189 333 443 476 511 18 200 211 211 ...
  ..$ qend         : int [1:8922] 461 1095 1093 1054 1088 1049 461 325 318 279 ...
  ..$ tstart       : int [1:8922] 16 133 131 190 23 296 16 864 527 767 ...
  ..$ tend         : int [1:8922] 425 989 910 804 638 834 425 989 638 834 ...
  ..$ evalue       : num [1:8922] 2.17e-58 3.80e-271 6.99e-72 3.09e-60 9.12e-51 ...
  ..$ bitscore     : num [1:8922] 199 791 257 221 192 178 199 162 62.4 59.7 ...
 $ Bprasinos_PicRCC4223               :'data.frame':    6901 obs. of  12 variables:
  ..$ query        : chr [1:6901] "Bpra_BPRRCC1105_00G00020" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" ...
  ..$ db           : chr [1:6901] "PicR_RCC4223.05g02230" "PicR_RCC4223.02g06220" "PicR_RCC4223.02g10050" "PicR_RCC4223.11g00290" ...
  ..$ perc_identity: num [1:6901] 30.9 37.7 28 30.2 28.3 24.3 30.9 55.4 43.4 35.9 ...
  ..$ length       : int [1:6901] 278 771 624 556 669 544 278 121 76 128 ...
  ..$ mismatches   : int [1:6901] 134 425 352 316 396 358 134 49 43 73 ...
  ..$ gap_open     : int [1:6901] 7 14 13 13 17 15 7 1 0 3 ...
  ..$ qstart       : int [1:6901] 190 346 511 518 469 535 190 204 211 200 ...
  ..$ qend         : int [1:6901] 461 1089 1068 1045 1089 1044 461 319 286 319 ...
  ..$ tstart       : int [1:6901] 133 125 389 286 239 148 133 747 685 745 ...
  ..$ tend         : int [1:6901] 358 867 981 797 871 671 358 867 760 871 ...
  ..$ evalue       : num [1:6901] 6.53e-25 1.06e-126 3.37e-53 2.58e-50 1.23e-48 ...
  ..$ bitscore     : num [1:6901] 105 410 201 191 186 78.2 105 106 62 57.4 ...
 $ Bprasinos_PicSE3                   :'data.frame':    6574 obs. of  12 variables:
  ..$ query        : chr [1:6574] "Bpra_BPRRCC1105_00G00020" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" ...
  ..$ db           : chr [1:6574] "PicS_PI00G14680" "PicS_PI00G15990" "PicS_PI00G10800" "PicS_PI00G55600" ...
  ..$ perc_identity: num [1:6574] 32.4 36.9 28 29.3 29.6 24.1 32.4 58.2 43.4 38.5 ...
  ..$ length       : int [1:6574] 281 788 625 665 558 547 281 110 76 117 ...
  ..$ mismatches   : int [1:6574] 129 442 351 394 317 355 129 46 43 68 ...
  ..$ gap_open     : int [1:6574] 8 15 13 18 18 14 8 0 0 2 ...
  ..$ qstart       : int [1:6574] 190 329 511 469 518 535 190 210 211 206 ...
  ..$ qend         : int [1:6574] 461 1089 1068 1089 1045 1044 461 319 286 319 ...
  ..$ tstart       : int [1:6574] 80 107 392 45 275 148 80 757 685 562 ...
  ..$ tend         : int [1:6574] 308 866 984 677 786 671 308 866 760 677 ...
  ..$ evalue       : num [1:6574] 1.35e-27 1.51e-123 3.02e-54 6.44e-51 4.71e-50 ...
  ..$ bitscore     : num [1:6574] 112 402 204 190 189 76.3 112 105 62 57 ...
 $ Bprasinos_Ppatens                  :'data.frame':    10685 obs. of  12 variables:
  ..$ query        : chr [1:10685] "Bpra_BPRRCC1105_00G00020" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" ...
  ..$ db           : chr [1:10685] "Ppat_PP00001G03400" "Ppat_PP00237G00410" "Ppat_PP00053G00970" "Ppat_PP00019G01200" ...
  ..$ perc_identity: num [1:10685] 29.1 42.6 41.6 32 28.3 28.7 29.1 64 63.2 44.8 ...
  ..$ length       : int [1:10685] 447 748 748 579 775 778 447 111 114 87 ...
  ..$ mismatches   : int [1:10685] 213 371 375 324 439 430 213 40 42 45 ...
  ..$ gap_open     : int [1:10685] 14 12 14 13 20 20 14 0 0 2 ...
  ..$ qstart       : int [1:10685] 22 345 344 510 347 347 22 209 209 195 ...
  ..$ qend         : int [1:10685] 461 1092 1089 1063 1049 1049 461 319 322 279 ...
  ..$ tstart       : int [1:10685] 11 268 283 382 217 214 11 860 844 856 ...
  ..$ tend         : int [1:10685] 360 957 970 915 946 941 360 970 957 941 ...
  ..$ evalue       : num [1:10685] 1.78e-38 1.07e-153 2.63e-152 6.40e-60 6.30e-59 ...
  ..$ bitscore     : num [1:10685] 145 492 493 223 220 220 145 134 132 60.8 ...
 $ Bprasinos_Vcarteri                 :'data.frame':    7059 obs. of  12 variables:
  ..$ query        : chr [1:7059] "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" "Bpra_BPRRCC1105_00G00030" ...
  ..$ db           : chr [1:7059] "Vcar_VC00G90350" "Vcar_VC00G04670" "Vcar_VC00G77240" "Vcar_VC00G04660" ...
  ..$ perc_identity: num [1:7059] 27.3 24.6 28.3 22.8 26.8 35.3 38.9 50 55.6 36.6 ...
  ..$ length       : int [1:7059] 653 557 184 574 190 116 72 64 54 82 ...
  ..$ mismatches   : int [1:7059] 321 343 111 368 113 73 44 31 23 50 ...
  ..$ gap_open     : int [1:7059] 18 18 4 16 3 2 0 1 1 2 ...
  ..$ qstart       : int [1:7059] 563 535 887 535 889 203 212 211 206 202 ...
  ..$ qend         : int [1:7059] 1088 1044 1053 1060 1053 318 283 274 259 283 ...
  ..$ tstart       : int [1:7059] 397 105 619 152 652 909 727 1257 747 761 ...
  ..$ tend         : int [1:7059] 1022 631 798 698 840 1022 798 1319 799 840 ...
  ..$ evalue       : num [1:7059] 2.61e-36 7.69e-15 1.79e-12 3.52e-11 8.17e-09 ...
  ..$ bitscore     : num [1:7059] 148 79 71.2 67 59.3 59.7 53.9 51.6 50.8 50.4 ...
 $ Chlorellasp_Aprotothecoides        :'data.frame':    10546 obs. of  12 variables:
  ..$ query        : chr [1:10546] "Chlo_CNC64A_001G00050" "Chlo_CNC64A_001G00050" "Chlo_CNC64A_001G00060" "Chlo_CNC64A_001G00090" ...
  ..$ db           : chr [1:10546] "Apro_AP00G36640" "Apro_AP00G51240" "Apro_AP00G36630" "Apro_AP00G36600" ...
  ..$ perc_identity: num [1:10546] 65.9 62 49.2 69.8 40.5 48.1 39 31.9 25.2 55.4 ...
  ..$ length       : int [1:10546] 548 527 307 189 439 374 336 339 389 83 ...
  ..$ mismatches   : int [1:10546] 168 182 150 55 214 157 176 183 192 35 ...
  ..$ gap_open     : int [1:10546] 6 6 3 1 10 8 9 9 10 2 ...
  ..$ qstart       : int [1:10546] 1 20 33 1 52 1 1 3 3 5 ...
  ..$ qend         : int [1:10546] 534 532 337 189 480 339 320 321 329 86 ...
  ..$ tstart       : int [1:10546] 1 8 26 1 15 1 1 23 73 30 ...
  ..$ tend         : int [1:10546] 543 530 328 187 416 372 323 333 424 111 ...
  ..$ evalue       : num [1:10546] 2.10e-255 6.74e-228 2.78e-99 3.27e-83 1.55e-73 ...
  ..$ bitscore     : num [1:10546] 707 637 299 242 261 284 190 121 97.1 86.3 ...
 $ Chlorellasp_Asterochlorissp        :'data.frame':    11925 obs. of  12 variables:
  ..$ query        : chr [1:11925] "Chlo_CNC64A_001G00020" "Chlo_CNC64A_001G00040" "Chlo_CNC64A_001G00050" "Chlo_CNC64A_001G00050" ...
  ..$ db           : chr [1:11925] "Aste_AC00G55040" "Aste_AC00G54990" "Aste_AC00G25460" "Aste_AC00G25450" ...
  ..$ perc_identity: num [1:11925] 44.7 46.6 47.4 54.8 53.1 38.4 33.1 34 32.9 74.9 ...
  ..$ length       : int [1:11925] 264 670 312 230 371 383 338 368 356 311 ...
  ..$ mismatches   : int [1:11925] 131 278 111 103 123 157 182 171 201 77 ...
  ..$ gap_open     : int [1:11925] 5 9 4 1 7 8 8 9 12 1 ...
  ..$ qstart       : int [1:11925] 26 437 21 306 1 1 4 3 5 1 ...
  ..$ qend         : int [1:11925] 284 1103 287 535 336 336 334 340 336 311 ...
  ..$ tstart       : int [1:11925] 2 5 5 6 1 1 8 26 16 5 ...
  ..$ tend         : int [1:11925] 255 597 308 234 355 351 308 351 357 314 ...
  ..$ evalue       : num [1:11925] 1.07e-69 5.01e-175 3.39e-87 4.27e-85 3.36e-89 ...
  ..$ bitscore     : num [1:11925] 215 525 270 262 270 207 152 134 132 484 ...
 $ Chlorellasp_Bprasinos              :'data.frame':    7585 obs. of  12 variables:
  ..$ query        : chr [1:7585] "Chlo_CNC64A_001G00040" "Chlo_CNC64A_001G00090" "Chlo_CNC64A_001G00150" "Chlo_CNC64A_001G00150" ...
  ..$ db           : chr [1:7585] "Bpra_BPRRCC1105_03G04720" "Bpra_BPRRCC1105_12G03380" "Bpra_BPRRCC1105_16G00510" "Bpra_BPRRCC1105_01G06460" ...
  ..$ perc_identity: num [1:7585] 33.4 46.7 44.4 29.7 33.7 28.9 30.1 58.5 58.9 61.5 ...
  ..$ length       : int [1:7585] 928 210 347 380 359 329 349 289 285 65 ...
  ..$ mismatches   : int [1:7585] 444 90 160 157 158 188 202 118 115 23 ...
  ..$ gap_open     : int [1:7585] 17 3 7 7 10 7 6 1 1 1 ...
  ..$ qstart       : int [1:7585] 274 1 2 6 3 5 3 5 9 61 ...
  ..$ qend         : int [1:7585] 1103 188 336 321 322 302 332 293 293 125 ...
  ..$ tstart       : int [1:7585] 166 67 3 37 138 16 127 365 369 50 ...
  ..$ tend         : int [1:7585] 1017 276 328 370 455 329 452 651 651 112 ...
  ..$ evalue       : num [1:7585] 6.59e-129 1.51e-51 5.40e-69 4.50e-35 4.07e-32 ...
  ..$ bitscore     : num [1:7585] 417 165 217 131 123 113 106 356 352 90.9 ...
 $ Chlorellasp_Chlorellasp            :'data.frame':    19387 obs. of  12 variables:
  ..$ query        : chr [1:19387] "Chlo_CNC64A_001G00010" "Chlo_CNC64A_001G00010" "Chlo_CNC64A_001G00020" "Chlo_CNC64A_001G00030" ...
  ..$ db           : chr [1:19387] "Chlo_CNC64A_001G00010" "Chlo_CNC64A_004G00500" "Chlo_CNC64A_001G00020" "Chlo_CNC64A_001G00030" ...
  ..$ perc_identity: num [1:19387] 100 62.4 100 100 100 100 58.4 100 100 46.9 ...
  ..$ length       : int [1:19387] 414 85 285 347 1103 535 527 369 472 341 ...
  ..$ mismatches   : int [1:19387] 0 23 0 0 0 0 182 0 0 130 ...
  ..$ gap_open     : int [1:19387] 0 2 0 0 0 0 7 0 0 9 ...
  ..$ qstart       : int [1:19387] 1 34 1 1 1 1 20 1 1 1 ...
  ..$ qend         : int [1:19387] 414 117 285 347 1103 535 532 369 472 329 ...
  ..$ tstart       : int [1:19387] 1 138 1 1 1 1 8 1 1 84 ...
  ..$ tend         : int [1:19387] 414 214 285 347 1103 535 511 369 472 385 ...
  ..$ evalue       : num [1:19387] 1.14e-127 2.22e-06 1.73e-208 1.08e-194 0.00 ...
  ..$ bitscore     : num [1:19387] 375 48.5 567 538 1874 ...
 $ Chlorellasp_Creinhardtii           :'data.frame':    12805 obs. of  12 variables:
  ..$ query        : chr [1:12805] "Chlo_CNC64A_001G00020" "Chlo_CNC64A_001G00020" "Chlo_CNC64A_001G00040" "Chlo_CNC64A_001G00040" ...
  ..$ db           : chr [1:12805] "Crei_CR12G04850" "Crei_CR08G05900" "Crei_CR06G13360" "Crei_CR14G00950" ...
  ..$ perc_identity: num [1:12805] 58.4 39.1 36.7 22.8 51.5 38.8 42.6 48 61.4 40.5 ...
  ..$ length       : int [1:12805] 267 284 652 556 534 415 176 123 189 220 ...
  ..$ mismatches   : int [1:12805] 97 143 169 318 235 158 83 54 68 128 ...
  ..$ gap_open     : int [1:12805] 3 7 11 20 7 9 4 5 2 3 ...
  ..$ qstart       : int [1:12805] 22 22 664 259 20 36 213 269 1 70 ...
  ..$ qend         : int [1:12805] 285 285 1103 772 531 355 370 381 188 287 ...
  ..$ tstart       : int [1:12805] 49 643 1017 202 8 16 14 14 1 43 ...
  ..$ tend         : int [1:12805] 304 916 1636 688 539 429 189 136 185 261 ...
  ..$ evalue       : num [1:12805] 2.62e-101 1.45e-43 1.21e-94 2.55e-10 4.74e-172 ...
  ..$ bitscore     : num [1:12805] 298 158 332 65.1 497 242 146 113 209 153 ...
 $ Chlorellasp_Csubellipsoidea        :'data.frame':    12036 obs. of  12 variables:
  ..$ query        : chr [1:12036] "Chlo_CNC64A_001G00040" "Chlo_CNC64A_001G00050" "Chlo_CNC64A_001G00060" "Chlo_CNC64A_001G00140" ...
  ..$ db           : chr [1:12036] "Csub_CV00G17040" "Csub_CV00G04690" "Csub_CV00G15180" "Csub_CV00G15970" ...
  ..$ perc_identity: num [1:12036] 39.6 55.8 40.7 41.2 57.8 48.9 35.2 32.7 58.7 77.7 ...
  ..$ length       : int [1:12036] 891 529 391 211 351 348 332 352 75 305 ...
  ..$ mismatches   : int [1:12036] 411 198 207 108 129 147 193 182 28 67 ...
  ..$ gap_open     : int [1:12036] 14 5 4 3 4 8 10 9 1 1 ...
  ..$ qstart       : int [1:12036] 239 31 1 121 1 1 5 3 4 6 ...
  ..$ qend         : int [1:12036] 1103 532 369 330 339 336 320 329 78 310 ...
  ..$ tstart       : int [1:12036] 11 5 47 1 1 1 11 6 94 5 ...
  ..$ tend         : int [1:12036] 800 524 434 196 344 329 336 327 165 308 ...
  ..$ evalue       : num [1:12036] 1.56e-167 3.46e-201 4.81e-79 3.19e-39 3.93e-103 ...
  ..$ bitscore     : num [1:12036] 512 569 259 143 305 250 139 114 87.8 489 ...
 $ Chlorellasp_Helicosporidiumsp      :'data.frame':    7248 obs. of  12 variables:
  ..$ query        : chr [1:7248] "Chlo_CNC64A_001G00050" "Chlo_CNC64A_001G00050" "Chlo_CNC64A_001G00050" "Chlo_CNC64A_001G00060" ...
  ..$ db           : chr [1:7248] "Heli_HE0000G43310" "Heli_HE0000G41510" "Heli_HE0000G29840" "Heli_HE0000G41520" ...
  ..$ perc_identity: num [1:7248] 56.3 61.2 55.9 47.1 52.1 31.4 60.5 51.4 49.3 37.5 ...
  ..$ length       : int [1:7248] 536 381 93 325 349 344 76 74 75 120 ...
  ..$ mismatches   : int [1:7248] 199 116 39 146 129 189 27 34 37 68 ...
  ..$ gap_open     : int [1:7248] 7 5 1 5 9 9 1 1 1 1 ...
  ..$ qstart       : int [1:7248] 20 31 442 70 1 5 3 5 5 27 ...
  ..$ qend         : int [1:7248] 532 388 534 369 326 320 78 78 78 139 ...
  ..$ tstart       : int [1:7248] 11 21 1 6 1 38 65 31 13 421 ...
  ..$ tend         : int [1:7248] 534 392 91 329 334 362 137 102 87 540 ...
  ..$ evalue       : num [1:7248] 4.04e-210 2.66e-161 4.00e-25 1.11e-83 1.07e-104 ...
  ..$ bitscore     : num [1:7248] 592 462 96.7 264 308 118 90.9 80.9 72.8 67 ...
 $ Chlorellasp_Mpusilla               :'data.frame':    8993 obs. of  12 variables:
  ..$ query        : chr [1:8993] "Chlo_CNC64A_001G00020" "Chlo_CNC64A_001G00040" "Chlo_CNC64A_001G00090" "Chlo_CNC64A_001G00150" ...
  ..$ db           : chr [1:8993] "Mpus_MP10G03370" "Mpus_MP03G05280" "Mpus_MP15G01690" "Mpus_MP14G00760" ...
  ..$ perc_identity: num [1:8993] 41.4 35.8 46.7 43.6 44.3 34.6 32.3 26.6 57.4 61.5 ...
  ..$ length       : int [1:8993] 309 917 225 321 359 318 341 335 305 65 ...
  ..$ mismatches   : int [1:8993] 144 420 87 161 157 179 196 196 125 23 ...
  ..$ gap_open     : int [1:8993] 9 19 2 5 11 4 7 7 3 1 ...
  ..$ qstart       : int [1:8993] 7 255 1 2 1 4 5 4 5 61 ...
  ..$ qend         : int [1:8993] 285 1103 192 321 320 321 320 320 306 125 ...
  ..$ tstart       : int [1:8993] 96 182 19 9 1 2 16 54 389 46 ...
  ..$ tend         : int [1:8993] 397 997 243 310 355 290 346 356 691 108 ...
  ..$ evalue       : num [1:8993] 1.58e-53 7.31e-145 4.78e-55 4.68e-66 4.91e-52 ...
  ..$ bitscore     : num [1:8993] 177 459 174 210 175 165 124 99.4 353 90.9 ...
 $ Chlorellasp_Msp                    :'data.frame':    9136 obs. of  12 variables:
  ..$ query        : chr [1:9136] "Chlo_CNC64A_001G00020" "Chlo_CNC64A_001G00090" "Chlo_CNC64A_001G00150" "Chlo_CNC64A_001G00150" ...
  ..$ db           : chr [1:9136] "Msp_MRCC299_12G01560" "Msp_MRCC299_13G03330" "Msp_MRCC299_15G02830" "Msp_MRCC299_12G03430" ...
  ..$ perc_identity: num [1:9136] 45.8 59.3 44.7 43.1 32.1 29 30.5 59.5 61.5 48.7 ...
  ..$ length       : int [1:9136] 319 194 358 353 324 365 351 289 65 113 ...
  ..$ mismatches   : int [1:9136] 117 72 148 179 181 177 198 115 23 54 ...
  ..$ gap_open     : int [1:9136] 6 4 7 10 6 6 8 1 1 2 ...
  ..$ qstart       : int [1:9136] 9 1 2 3 4 5 4 5 61 122 ...
  ..$ qend         : int [1:9136] 285 189 336 336 322 320 335 293 125 230 ...
  ..$ tstart       : int [1:9136] 93 30 7 6 2 12 27 381 56 2 ...
  ..$ tend         : int [1:9136] 397 221 337 355 291 343 350 667 118 114 ...
  ..$ evalue       : num [1:9136] 1.36e-78 4.85e-63 1.09e-69 2.10e-64 5.96e-39 ...
  ..$ bitscore     : num [1:9136] 242 193 219 206 139 130 127 359 90.9 97.4 ...
 $ Chlorellasp_Olucimarinus           :'data.frame':    8164 obs. of  12 variables:
  ..$ query        : chr [1:8164] "Chlo_CNC64A_001G00020" "Chlo_CNC64A_001G00040" "Chlo_CNC64A_001G00090" "Chlo_CNC64A_001G00150" ...
  ..$ db           : chr [1:8164] "Oluc_OL08G03570" "Oluc_OL05G03930" "Oluc_OL20G01110" "Oluc_OL12G00520" ...
  ..$ perc_identity: num [1:8164] 31.8 37.4 59.4 45.7 42.3 29.3 32 58.4 56.9 45.5 ...
  ..$ length       : int [1:8164] 198 928 187 359 326 355 356 77 65 123 ...
  ..$ mismatches   : int [1:8164] 113 419 74 144 171 221 162 29 26 63 ...
  ..$ gap_open     : int [1:8164] 3 25 1 6 7 6 9 1 1 2 ...
  ..$ qstart       : int [1:8164] 98 232 1 2 1 6 4 2 61 122 ...
  ..$ qend         : int [1:8164] 282 1103 187 335 320 336 320 78 125 240 ...
  ..$ tstart       : int [1:8164] 112 85 10 6 1 16 30 3 55 65 ...
  ..$ tend         : int [1:8164] 300 906 194 338 315 364 344 76 117 187 ...
  ..$ evalue       : num [1:8164] 4.95e-19 4.32e-145 4.59e-65 4.01e-69 1.97e-49 ...
  ..$ bitscore     : num [1:8164] 83.2 456 197 218 166 132 110 89.7 85.1 93.6 ...
 $ Chlorellasp_Omediterraneus         :'data.frame':    8020 obs. of  12 variables:
  ..$ query        : chr [1:8020] "Chlo_CNC64A_001G00020" "Chlo_CNC64A_001G00040" "Chlo_CNC64A_001G00090" "Chlo_CNC64A_001G00150" ...
  ..$ db           : chr [1:8020] "Omed_OM_11G01460" "Omed_OM_03G04190" "Omed_OM_13G02390" "Omed_OM_07G00480" ...
  ..$ perc_identity: num [1:8020] 37.5 37.1 57.4 41.1 43.3 32.1 36 61.6 56.6 55.4 ...
  ..$ length       : int [1:8020] 280 903 188 358 335 343 322 73 295 65 ...
  ..$ mismatches   : int [1:8020] 123 415 78 163 161 194 190 22 126 27 ...
  ..$ gap_open     : int [1:8020] 9 22 1 9 7 9 8 1 1 1 ...
  ..$ qstart       : int [1:8020] 23 256 1 2 3 6 4 4 4 61 ...
  ..$ qend         : int [1:8020] 284 1103 188 338 315 320 321 76 298 125 ...
  ..$ tstart       : int [1:8020] 53 55 14 7 5 17 39 25 371 33 ...
  ..$ tend         : int [1:8020] 298 859 199 337 332 348 348 91 663 95 ...
  ..$ evalue       : num [1:8020] 8.68e-44 5.60e-145 1.19e-64 5.37e-67 1.53e-48 ...
  ..$ bitscore     : num [1:8020] 149 455 196 212 165 136 110 89 355 83.6 ...
 $ Chlorellasp_Osp                    :'data.frame':    7719 obs. of  12 variables:
  ..$ query        : chr [1:7719] "Chlo_CNC64A_001G00040" "Chlo_CNC64A_001G00090" "Chlo_CNC64A_001G00150" "Chlo_CNC64A_001G00150" ...
  ..$ db           : chr [1:7719] "Osp_ORCC809_05G03860" "Osp_ORCC809_20G01110" "Osp_ORCC809_08G03200" "Osp_ORCC809_05G04360" ...
  ..$ perc_identity: num [1:7719] 37.2 60.4 47.1 41.2 30.2 34.4 59.7 58.5 35 38.8 ...
  ..$ length       : int [1:7719] 858 187 333 342 338 355 77 65 140 129 ...
  ..$ mismatches   : int [1:7719] 413 72 159 169 205 153 28 25 67 56 ...
  ..$ gap_open     : int [1:7719] 15 1 4 7 7 11 1 1 6 4 ...
  ..$ qstart       : int [1:7719] 275 2 2 6 6 5 2 61 104 115 ...
  ..$ qend         : int [1:7719] 1103 188 320 320 320 320 78 125 230 230 ...
  ..$ tstart       : int [1:7719] 4 21 6 10 16 1 2 44 46 5 ...
  ..$ tend         : int [1:7719] 764 205 335 346 345 314 75 106 174 123 ...
  ..$ evalue       : num [1:7719] 1.65e-147 8.76e-67 8.63e-65 2.19e-49 2.36e-33 ...
  ..$ bitscore     : num [1:7719] 458 201 207 167 125 102 93.6 86.7 63.2 61.6 ...
 $ Chlorellasp_Otauri                 :'data.frame':    7905 obs. of  12 variables:
  ..$ query        : chr [1:7905] "Chlo_CNC64A_001G00040" "Chlo_CNC64A_001G00090" "Chlo_CNC64A_001G00150" "Chlo_CNC64A_001G00150" ...
  ..$ db           : chr [1:7905] "Otau_OT_05G04010" "Otau_OT_14G01160" "Otau_OT_12G00410" "Otau_OT_05G04560" ...
  ..$ perc_identity: num [1:7905] 37.3 61.4 42.1 41.1 29.2 34 58.4 60.6 60 28.8 ...
  ..$ length       : int [1:7905] 896 189 359 336 342 356 77 279 65 313 ...
  ..$ mismatches   : int [1:7905] 400 71 157 178 205 157 29 108 24 171 ...
  ..$ gap_open     : int [1:7905] 22 1 5 6 6 11 1 1 1 8 ...
  ..$ qstart       : int [1:7905] 260 1 2 1 6 4 2 14 61 36 ...
  ..$ qend         : int [1:7905] 1103 189 336 322 320 320 78 292 125 323 ...
  ..$ tstart       : int [1:7905] 105 1 8 1 17 34 21 373 45 48 ...
  ..$ tend         : int [1:7905] 890 187 339 330 348 350 94 649 107 333 ...
  ..$ evalue       : num [1:7905] 5.40e-148 4.75e-68 7.52e-68 7.12e-52 1.48e-34 ...
  ..$ bitscore     : num [1:7905] 464 204 214 173 129 112 90.5 357 88.6 92.8 ...
 $ Chlorellasp_PicRCC4223             :'data.frame':    10908 obs. of  12 variables:
  ..$ query        : chr [1:10908] "Chlo_CNC64A_001G00030" "Chlo_CNC64A_001G00040" "Chlo_CNC64A_001G00060" "Chlo_CNC64A_001G00090" ...
  ..$ db           : chr [1:10908] "PicR_RCC4223.01g04030" "PicR_RCC4223.01g04050" "PicR_RCC4223.30g00210" "PicR_RCC4223.01g04230" ...
  ..$ perc_identity: num [1:10908] 50 40.6 33.6 56.9 29.9 26.5 58.9 31.7 33.7 35 ...
  ..$ length       : int [1:10908] 54 924 220 197 298 483 341 369 347 334 ...
  ..$ mismatches   : int [1:10908] 26 427 135 72 175 261 108 169 197 182 ...
  ..$ gap_open     : int [1:10908] 1 20 2 3 10 9 7 13 9 11 ...
  ..$ qstart       : int [1:10908] 172 208 145 1 35 801 1 3 5 5 ...
  ..$ qend         : int [1:10908] 225 1103 353 187 311 1238 325 332 330 334 ...
  ..$ tstart       : int [1:10908] 60 30 81 30 2 311 1 26 28 59 ...
  ..$ tend         : int [1:10908] 112 859 300 223 286 744 325 350 362 361 ...
  ..$ evalue       : num [1:10908] 4.89e-12 5.57e-184 5.83e-38 2.14e-65 4.95e-20 ...
  ..$ bitscore     : num [1:10908] 62.4 557 139 199 91.3 70.9 340 121 122 98.6 ...
 $ Chlorellasp_PicSE3                 :'data.frame':    10476 obs. of  12 variables:
  ..$ query        : chr [1:10476] "Chlo_CNC64A_001G00030" "Chlo_CNC64A_001G00040" "Chlo_CNC64A_001G00090" "Chlo_CNC64A_001G00140" ...
  ..$ db           : chr [1:10476] "PicS_PI00G47100" "PicS_PI00G47110" "PicS_PI00G47270" "PicS_PI00G12810" ...
  ..$ perc_identity: num [1:10476] 52 41.8 57.4 31.8 28.4 58.8 32 33.4 31.6 30.5 ...
  ..$ length       : int [1:10476] 50 910 195 274 486 340 369 347 339 394 ...
  ..$ mismatches   : int [1:10476] 23 420 71 155 247 113 168 198 187 182 ...
  ..$ gap_open     : int [1:10476] 1 22 2 9 7 6 13 9 11 11 ...
  ..$ qstart       : int [1:10476] 172 220 1 35 801 1 3 5 5 3 ...
  ..$ qend         : int [1:10476] 221 1103 187 287 1238 325 332 330 334 335 ...
  ..$ tstart       : int [1:10476] 56 34 30 35 321 1 26 28 59 72 ...
  ..$ tend         : int [1:10476] 104 859 220 297 753 328 350 362 361 434 ...
  ..$ evalue       : num [1:10476] 7.18e-11 3.97e-182 1.52e-68 9.13e-20 3.27e-13 ...
  ..$ bitscore     : num [1:10476] 58.5 552 206 89.7 72.4 342 122 120 101 94.7 ...
 $ Chlorellasp_Ppatens                :'data.frame':    14620 obs. of  12 variables:
  ..$ query        : chr [1:14620] "Chlo_CNC64A_001G00030" "Chlo_CNC64A_001G00040" "Chlo_CNC64A_001G00050" "Chlo_CNC64A_001G00060" ...
  ..$ db           : chr [1:14620] "Ppat_PP00131G01010" "Ppat_PP00134G00190" "Ppat_PP00040G00040" "Ppat_PP00116G00050" ...
  ..$ perc_identity: num [1:14620] 41.5 34.9 49.2 41.6 40.5 42.6 41.1 42.1 42 43.1 ...
  ..$ length       : int [1:14620] 53 559 551 368 368 359 353 361 355 339 ...
  ..$ mismatches   : int [1:14620] 31 280 242 211 215 170 170 172 166 173 ...
  ..$ gap_open     : int [1:14620] 0 16 7 2 2 7 6 7 7 6 ...
  ..$ qstart       : int [1:14620] 172 415 12 2 2 1 1 1 1 1 ...
  ..$ qend         : int [1:14620] 224 962 534 369 369 336 327 336 327 327 ...
  ..$ tstart       : int [1:14620] 26 651 14 68 71 1 1 1 1 1 ...
  ..$ tend         : int [1:14620] 78 1136 554 431 434 346 341 349 343 331 ...
  ..$ evalue       : num [1:14620] 5.30e-09 5.91e-77 1.12e-172 1.81e-92 1.64e-87 ...
  ..$ bitscore     : num [1:14620] 55.1 276 499 285 272 249 238 238 236 232 ...
 $ Chlorellasp_Vcarteri               :'data.frame':    11215 obs. of  12 variables:
  ..$ query        : chr [1:11215] "Chlo_CNC64A_001G00020" "Chlo_CNC64A_001G00020" "Chlo_CNC64A_001G00040" "Chlo_CNC64A_001G00050" ...
  ..$ db           : chr [1:11215] "Vcar_VC00G99500" "Vcar_VC00G82260" "Vcar_VC00G12030" "Vcar_VC00G46810" ...
  ..$ perc_identity: num [1:11215] 55.6 37.5 38 51.6 62.6 54 34.4 32.7 33.9 37.4 ...
  ..$ length       : int [1:11215] 279 291 637 533 174 324 320 523 354 350 ...
  ..$ mismatches   : int [1:11215] 110 150 166 220 60 121 181 157 199 173 ...
  ..$ gap_open     : int [1:11215] 3 7 8 8 2 6 5 14 11 7 ...
  ..$ qstart       : int [1:11215] 10 22 664 20 1 1 2 1 5 2 ...
  ..$ qend         : int [1:11215] 285 285 1103 523 173 320 320 336 336 333 ...
  ..$ tstart       : int [1:11215] 39 658 1015 8 1 1 4 1 17 3 ...
  ..$ tend         : int [1:11215] 306 943 1619 531 170 300 295 515 357 324 ...
  ..$ evalue       : num [1:11215] 1.52e-97 6.29e-48 2.81e-98 9.32e-171 3.30e-65 ...
  ..$ bitscore     : num [1:11215] 288 170 342 493 197 272 175 143 135 125 ...
 $ Creinhardtii_Aprotothecoides       :'data.frame':    12142 obs. of  12 variables:
  ..$ query        : chr [1:12142] "Crei_CR00G00420" "Crei_CR00G00420" "Crei_CR00G00420" "Crei_CR00G00420" ...
  ..$ db           : chr [1:12142] "Apro_AP00G07160" "Apro_AP00G49530" "Apro_AP00G30060" "Apro_AP00G19780" ...
  ..$ perc_identity: num [1:12142] 36.6 33.2 38.9 35.1 32.7 41.3 58.3 51 25.5 65.3 ...
  ..$ length       : int [1:12142] 235 217 167 228 214 378 132 147 404 98 ...
  ..$ mismatches   : int [1:12142] 131 134 76 106 110 166 52 52 201 34 ...
  ..$ gap_open     : int [1:12142] 4 5 4 9 7 7 2 2 9 0 ...
  ..$ qstart       : int [1:12142] 272 278 329 293 291 52 1 582 342 341 ...
  ..$ qend         : int [1:12142] 495 490 494 517 503 425 129 728 728 438 ...
  ..$ tstart       : int [1:12142] 269 614 467 474 454 146 1 76 139 260 ...
  ..$ tend         : int [1:12142] 496 823 608 662 634 471 132 202 459 357 ...
  ..$ evalue       : num [1:12142] 2.74e-34 3.70e-27 6.94e-24 3.83e-23 5.86e-20 ...
  ..$ bitscore     : num [1:12142] 135 115 104 102 92.4 249 148 128 81.3 128 ...
 $ Creinhardtii_Asterochlorissp       :'data.frame':    16259 obs. of  12 variables:
  ..$ query        : chr [1:16259] "Crei_CR00G00030" "Crei_CR00G00420" "Crei_CR00G00420" "Crei_CR00G00420" ...
  ..$ db           : chr [1:16259] "Aste_AC00G98550" "Aste_AC00G32750" "Aste_AC00G93520" "Aste_AC00G71610" ...
  ..$ perc_identity: num [1:16259] 29.5 37 36.1 42 34.7 43.5 53 38.7 61.9 39.9 ...
  ..$ length       : int [1:16259] 492 216 208 169 225 138 287 401 126 469 ...
  ..$ mismatches   : int [1:16259] 246 118 112 93 119 71 124 201 47 195 ...
  ..$ gap_open     : int [1:16259] 17 6 5 4 7 3 2 11 1 7 ...
  ..$ qstart       : int [1:16259] 1097 293 290 326 291 337 141 53 5 164 ...
  ..$ qend         : int [1:16259] 1564 494 487 493 511 473 427 425 129 627 ...
  ..$ tstart       : int [1:16259] 202 1 537 42 294 1 2 53 2 54 ...
  ..$ tend         : int [1:16259] 616 212 733 206 494 132 277 436 127 440 ...
  ..$ evalue       : num [1:16259] 3.98e-28 1.16e-31 1.15e-30 1.72e-30 1.38e-29 ...
  ..$ bitscore     : num [1:16259] 120 122 127 118 122 111 278 221 163 286 ...
 $ Creinhardtii_Bprasinos             :'data.frame':    10352 obs. of  12 variables:
  ..$ query        : chr [1:10352] "Crei_CR00G00030" "Crei_CR00G00420" "Crei_CR00G00420" "Crei_CR00G00420" ...
  ..$ db           : chr [1:10352] "Bpra_BPRRCC1105_11G02890" "Bpra_BPRRCC1105_01G05720" "Bpra_BPRRCC1105_13G02640" "Bpra_BPRRCC1105_08G04680" ...
  ..$ perc_identity: num [1:10352] 25.4 34.4 31.6 29.3 34 35.1 49.3 56.2 26.4 36.8 ...
  ..$ length       : int [1:10352] 503 209 231 215 159 114 280 89 387 76 ...
  ..$ mismatches   : int [1:10352] 288 99 115 122 88 60 129 36 207 46 ...
  ..$ gap_open     : int [1:10352] 20 7 10 7 5 2 4 3 8 2 ...
  ..$ qstart       : int [1:10352] 1097 315 291 293 329 321 153 44 347 582 ...
  ..$ qend         : int [1:10352] 1551 494 501 493 483 432 424 129 728 656 ...
  ..$ tstart       : int [1:10352] 48 550 908 977 611 396 49 81 327 304 ...
  ..$ tend         : int [1:10352] 511 749 1115 1175 756 497 323 169 640 378 ...
  ..$ evalue       : num [1:10352] 1.68e-20 2.59e-22 1.41e-20 1.55e-14 4.44e-13 ...
  ..$ bitscore     : num [1:10352] 96.7 100 95.9 76.3 71.2 67.4 238 102 81.3 50.4 ...
 $ Creinhardtii_Chlorellasp           :'data.frame':    15630 obs. of  12 variables:
  ..$ query        : chr [1:15630] "Crei_CR00G00420" "Crei_CR00G00420" "Crei_CR00G00420" "Crei_CR00G00420" ...
  ..$ db           : chr [1:15630] "Chlo_CNC64A_006G04120" "Chlo_CNC64A_003G04060" "Chlo_CNC64A_003G04630" "Chlo_CNC64A_011G01580" ...
  ..$ perc_identity: num [1:15630] 38.7 39.1 40 30.4 39.9 45.7 59.5 45.9 29.4 45.6 ...
  ..$ length       : int [1:15630] 238 233 210 467 198 398 126 503 218 79 ...
  ..$ mismatches   : int [1:15630] 128 127 117 232 110 196 50 188 87 40 ...
  ..$ gap_open     : int [1:15630] 5 6 5 15 3 6 1 10 5 1 ...
  ..$ qstart       : int [1:15630] 291 280 283 28 295 38 5 226 442 582 ...
  ..$ qend         : int [1:15630] 516 505 490 493 491 426 129 726 658 660 ...
  ..$ tstart       : int [1:15630] 1189 488 9 381 864 26 6 4 81 448 ...
  ..$ tend         : int [1:15630] 1420 712 211 755 1053 412 131 424 232 523 ...
  ..$ evalue       : num [1:15630] 3.83e-38 1.11e-37 3.81e-37 1.08e-36 2.37e-32 ...
  ..$ bitscore     : num [1:15630] 152 149 138 146 133 316 150 362 61.2 61.6 ...
 $ Creinhardtii_Creinhardtii          :'data.frame':    42697 obs. of  12 variables:
  ..$ query        : chr [1:42697] "Crei_CR00G00010" "Crei_CR00G00010" "Crei_CR00G00020" "Crei_CR00G00020" ...
  ..$ db           : chr [1:42697] "Crei_CR00G00010" "Crei_CR00G01920" "Crei_CR00G00020" "Crei_CR02G14450" ...
  ..$ perc_identity: num [1:42697] 100 75.6 100 100 75 100 98.1 100 58.3 97.3 ...
  ..$ length       : int [1:42697] 155 90 515 209 124 52 52 1654 2788 781 ...
  ..$ mismatches   : int [1:42697] 0 16 0 0 29 0 1 0 21 15 ...
  ..$ gap_open     : int [1:42697] 0 3 0 0 1 0 0 0 6 2 ...
  ..$ qstart       : int [1:42697] 1 1 1 307 307 307 14 1 1 872 ...
  ..$ qend         : int [1:42697] 155 84 515 515 430 358 65 1654 1649 1649 ...
  ..$ tstart       : int [1:42697] 1 1 1 488 485 127 195 1 1 1563 ...
  ..$ tend         : int [1:42697] 155 90 515 696 606 178 246 1654 2788 2340 ...
  ..$ evalue       : num [1:42697] 3.31e-108 4.80e-38 1.19e-126 3.83e-119 4.43e-44 ...
  ..$ bitscore     : num [1:42697] 304 125 379 365 167 ...
 $ Creinhardtii_Csubellipsoidea       :'data.frame':    15123 obs. of  12 variables:
  ..$ query        : chr [1:15123] "Crei_CR00G00420" "Crei_CR00G00420" "Crei_CR00G00420" "Crei_CR00G00420" ...
  ..$ db           : chr [1:15123] "Csub_CV00G26810" "Csub_CV00G53610" "Csub_CV00G20970" "Csub_CV00G20960" ...
  ..$ perc_identity: num [1:15123] 37.6 39.8 42.5 41.1 37.7 36.8 60.3 42.6 28.5 44 ...
  ..$ length       : int [1:15123] 242 201 214 202 220 391 126 563 291 84 ...
  ..$ mismatches   : int [1:15123] 127 113 108 107 125 184 49 208 139 44 ...
  ..$ gap_open     : int [1:15123] 4 3 7 3 3 8 1 9 7 3 ...
  ..$ qstart       : int [1:15123] 280 290 284 290 278 52 5 167 442 582 ...
  ..$ qend         : int [1:15123] 502 490 493 490 495 425 129 727 728 664 ...
  ..$ tstart       : int [1:15123] 314 455 810 604 296 66 2 1 161 212 ...
  ..$ tend         : int [1:15123] 550 647 1012 794 505 410 127 450 386 293 ...
  ..$ evalue       : num [1:15123] 7.00e-38 7.10e-36 3.97e-35 4.70e-35 4.78e-34 ...
  ..$ bitscore     : num [1:15123] 147 144 142 141 136 202 156 377 81.6 55.5 ...
 $ Creinhardtii_Helicosporidiumsp     :'data.frame':    8545 obs. of  12 variables:
  ..$ query        : chr [1:8545] "Crei_CR00G00030" "Crei_CR00G00420" "Crei_CR00G00420" "Crei_CR00G00420" ...
  ..$ db           : chr [1:8545] "Heli_HE0000G51900" "Heli_HE0000G03300" "Heli_HE0000G11450" "Heli_HE0000G28820" ...
  ..$ perc_identity: num [1:8545] 30.4 39.3 33.3 36.3 29.5 32.5 53 30.8 69.7 49.1 ...
  ..$ length       : int [1:8545] 519 173 213 157 156 354 132 240 221 108 ...
  ..$ mismatches   : int [1:8545] 263 74 117 61 88 169 59 112 67 54 ...
  ..$ gap_open     : int [1:8545] 19 7 4 6 4 8 2 10 0 1 ...
  ..$ qstart       : int [1:8545] 1097 337 284 295 276 73 1 434 26 582 ...
  ..$ qend         : int [1:8545] 1564 490 496 430 431 426 129 658 246 688 ...
  ..$ tstart       : int [1:8545] 208 1 85 1 52 13 1 134 150 5 ...
  ..$ tend         : int [1:8545] 679 161 272 139 185 296 132 334 370 112 ...
  ..$ evalue       : num [1:8545] 6.09e-32 3.63e-26 7.01e-24 3.06e-13 1.08e-11 ...
  ..$ bitscore     : num [1:8545] 131 103 100 66.2 62.4 142 135 61.2 321 100 ...
 $ Creinhardtii_Mpusilla              :'data.frame':    12369 obs. of  12 variables:
  ..$ query        : chr [1:12369] "Crei_CR00G00030" "Crei_CR00G00420" "Crei_CR00G00420" "Crei_CR00G00420" ...
  ..$ db           : chr [1:12369] "Mpus_MP07G00030" "Mpus_MP07G01470" "Mpus_MP05G05110" "Mpus_MP03G05440" ...
  ..$ perc_identity: num [1:12369] 33.2 36.5 39.4 31.7 34.1 29.9 43 54.3 27.1 30.9 ...
  ..$ length       : int [1:12369] 211 219 180 218 176 184 286 127 406 233 ...
  ..$ mismatches   : int [1:12369] 116 112 90 126 100 109 126 56 218 128 ...
  ..$ gap_open     : int [1:12369] 9 7 6 5 5 8 6 2 11 5 ...
  ..$ qstart       : int [1:12369] 1097 284 330 284 329 324 164 5 328 428 ...
  ..$ qend         : int [1:12369] 1298 496 499 499 501 497 426 129 728 658 ...
  ..$ tstart       : int [1:12369] 52 788 596 345 462 263 1 2 57 181 ...
  ..$ tend         : int [1:12369] 246 985 766 541 624 436 272 128 389 382 ...
  ..$ evalue       : num [1:12369] 5.24e-16 8.85e-27 4.25e-25 3.79e-24 7.23e-17 ...
  ..$ bitscore     : num [1:12369] 82.8 115 110 106 83.6 73.9 181 133 90.5 68.9 ...
 $ Creinhardtii_Msp                   :'data.frame':    12745 obs. of  12 variables:
  ..$ query        : chr [1:12745] "Crei_CR00G00420" "Crei_CR00G00420" "Crei_CR00G00420" "Crei_CR00G00420" ...
  ..$ db           : chr [1:12745] "Msp_MRCC299_13G01450" "Msp_MRCC299_07G00500" "Msp_MRCC299_05G04060" "Msp_MRCC299_04G02250" ...
  ..$ perc_identity: num [1:12745] 35.9 36.6 32.5 30.6 28.8 48.2 53 26.4 29.5 25.7 ...
  ..$ length       : int [1:12745] 223 224 209 229 212 284 115 397 224 214 ...
  ..$ mismatches   : int [1:12745] 116 129 118 139 117 139 53 214 117 104 ...
  ..$ gap_open     : int [1:12745] 7 7 5 6 8 3 1 11 4 5 ...
  ..$ qstart       : int [1:12745] 284 271 284 284 293 151 16 337 442 456 ...
  ..$ qend         : int [1:12745] 500 491 490 509 490 426 129 728 658 658 ...
  ..$ tstart       : int [1:12745] 770 747 250 176 319 151 15 155 204 126 ...
  ..$ tend         : int [1:12745] 971 960 437 387 510 434 129 478 393 295 ...
  ..$ evalue       : num [1:12745] 8.52e-28 2.47e-25 3.85e-25 6.98e-18 1.34e-14 ...
  ..$ bitscore     : num [1:12745] 119 111 108 85.5 75.9 234 123 82 65.9 54.3 ...
 $ Creinhardtii_Olucimarinus          :'data.frame':    11125 obs. of  12 variables:
  ..$ query        : chr [1:11125] "Crei_CR00G00030" "Crei_CR00G00420" "Crei_CR00G00420" "Crei_CR00G00420" ...
  ..$ db           : chr [1:11125] "Oluc_OL06G04060" "Oluc_OL12G01280" "Oluc_OL05G02420" "Oluc_OL11G02300" ...
  ..$ perc_identity: num [1:11125] 27.4 33.5 28.7 33.3 40.4 32.5 48.4 57.7 26.2 26.5 ...
  ..$ length       : int [1:11125] 511 209 209 177 151 166 283 123 389 226 ...
  ..$ mismatches   : int [1:11125] 262 109 125 94 59 90 138 49 205 109 ...
  ..$ gap_open     : int [1:11125] 23 6 5 7 6 5 4 2 10 4 ...
  ..$ qstart       : int [1:11125] 1097 291 284 325 291 329 145 8 347 442 ...
  ..$ qend         : int [1:11125] 1545 490 490 493 429 487 427 129 728 656 ...
  ..$ tstart       : int [1:11125] 61 101 188 95 152 114 38 2 162 135 ...
  ..$ tend         : int [1:11125] 524 288 374 255 283 264 312 122 475 314 ...
  ..$ evalue       : num [1:11125] 2.08e-22 6.08e-22 1.58e-21 1.80e-16 1.26e-15 ...
  ..$ bitscore     : num [1:11125] 102 95.9 95.9 78.2 77.4 70.1 246 142 77.8 58.2 ...
 $ Creinhardtii_Omediterraneus        :'data.frame':    10839 obs. of  12 variables:
  ..$ query        : chr [1:10839] "Crei_CR00G00030" "Crei_CR00G00420" "Crei_CR00G00420" "Crei_CR00G00420" ...
  ..$ db           : chr [1:10839] "Omed_OM_10G02100" "Omed_OM_10G00800" "Omed_OM_03G02620" "Omed_OM_07G01250" ...
  ..$ perc_identity: num [1:10839] 25.5 32.3 30.6 32.9 31.5 31.1 48.9 56.9 25.9 26.7 ...
  ..$ length       : int [1:10839] 478 223 209 210 216 180 274 123 394 225 ...
  ..$ mismatches   : int [1:10839] 246 128 122 109 113 93 127 50 210 111 ...
  ..$ gap_open     : int [1:10839] 18 5 5 8 8 7 3 2 10 3 ...
  ..$ qstart       : int [1:10839] 1134 284 284 291 291 327 154 8 342 442 ...
  ..$ qend         : int [1:10839] 1540 503 490 490 493 490 426 129 728 656 ...
  ..$ tstart       : int [1:10839] 110 379 339 480 635 785 45 2 276 188 ...
  ..$ tend         : int [1:10839] 548 581 526 667 828 949 306 122 594 368 ...
  ..$ evalue       : num [1:10839] 3.00e-14 2.37e-25 9.12e-22 1.81e-20 2.52e-19 ...
  ..$ bitscore     : num [1:10839] 76.3 109 98.2 94.7 91.3 75.9 239 140 77 58.9 ...
 $ Creinhardtii_Osp                   :'data.frame':    10465 obs. of  12 variables:
  ..$ query        : chr [1:10465] "Crei_CR00G00420" "Crei_CR00G00420" "Crei_CR00G00420" "Crei_CR00G00420" ...
  ..$ db           : chr [1:10465] "Osp_ORCC809_05G02410" "Osp_ORCC809_17G01250" "Osp_ORCC809_12G01750" "Osp_ORCC809_05G03130" ...
  ..$ perc_identity: num [1:10465] 30.1 31.2 32 36.5 29.3 48.5 56.9 29.5 26.3 26.9 ...
  ..$ length       : int [1:10465] 209 205 231 159 215 272 123 292 224 245 ...
  ..$ mismatches   : int [1:10465] 122 115 119 68 128 132 50 133 112 130 ...
  ..$ gap_open     : int [1:10465] 5 5 8 5 7 4 2 8 4 7 ...
  ..$ qstart       : int [1:10465] 284 292 291 287 283 154 8 442 442 426 ...
  ..$ qend         : int [1:10465] 490 490 504 433 490 425 129 728 656 658 ...
  ..$ tstart       : int [1:10465] 355 102 411 154 99 36 2 250 168 175 ...
  ..$ tend         : int [1:10465] 541 286 620 291 296 299 122 473 347 382 ...
  ..$ evalue       : num [1:10465] 3.83e-23 2.23e-22 1.50e-18 3.39e-16 8.82e-16 ...
  ..$ bitscore     : num [1:10465] 102 96.3 88.2 79.3 79.3 232 142 79.7 57.4 53.5 ...
 $ Creinhardtii_Otauri                :'data.frame':    10690 obs. of  12 variables:
  ..$ query        : chr [1:10690] "Crei_CR00G00420" "Crei_CR00G00420" "Crei_CR00G00420" "Crei_CR00G00420" ...
  ..$ db           : chr [1:10690] "Otau_OT_05G02490" "Otau_OT_05G03270" "Otau_OT_12G01170" "Otau_OT_04G05060" ...
  ..$ perc_identity: num [1:10690] 30.6 35.6 33.5 31.9 26.8 47 54.5 26.3 26.8 26.7 ...
  ..$ length       : int [1:10690] 209 236 209 182 213 281 123 395 224 247 ...
  ..$ mismatches   : int [1:10690] 121 111 109 98 123 140 53 209 111 124 ...
  ..$ gap_open     : int [1:10690] 6 8 6 6 7 3 2 10 3 8 ...
  ..$ qstart       : int [1:10690] 284 274 291 327 291 147 8 341 442 428 ...
  ..$ qend         : int [1:10690] 490 490 490 496 490 426 129 728 656 658 ...
  ..$ tstart       : int [1:10690] 344 439 473 720 597 30 2 278 167 176 ...
  ..$ tend         : int [1:10690] 530 652 660 887 789 302 122 597 346 381 ...
  ..$ evalue       : num [1:10690] 1.76e-23 3.60e-20 3.86e-20 1.03e-15 1.08e-14 ...
  ..$ bitscore     : num [1:10690] 103 93.6 93.6 79.7 76.3 241 137 81.6 60.8 53.9 ...
 $ Creinhardtii_PicRCC4223            :'data.frame':    12711 obs. of  12 variables:
  ..$ query        : chr [1:12711] "Crei_CR00G00030" "Crei_CR00G00030" "Crei_CR00G00030" "Crei_CR00G00030" ...
  ..$ db           : chr [1:12711] "PicR_RCC4223.10g03640" "PicR_RCC4223.08g00290" "PicR_RCC4223.06g00500" "PicR_RCC4223.19g00010" ...
  ..$ perc_identity: num [1:12711] 29.2 33.6 33.6 33.6 29.1 26.8 31 31 32.2 33.9 ...
  ..$ length       : int [1:12711] 455 146 146 146 230 198 100 100 211 236 ...
  ..$ mismatches   : int [1:12711] 237 78 78 78 158 140 68 68 120 132 ...
  ..$ gap_open     : int [1:12711] 17 3 3 3 2 2 1 1 4 7 ...
  ..$ qstart       : int [1:12711] 1097 1399 1399 1399 498 498 403 403 284 274 ...
  ..$ qend         : int [1:12711] 1547 1544 1544 1544 722 690 501 501 493 493 ...
  ..$ tstart       : int [1:12711] 196 157 292 293 355 355 390 390 401 215 ...
  ..$ tend         : int [1:12711] 569 283 418 419 584 552 489 489 589 442 ...
  ..$ evalue       : num [1:12711] 8.41e-27 1.40e-07 2.23e-07 2.24e-07 1.05e-21 ...
  ..$ bitscore     : num [1:12711] 115 53.5 53.5 53.5 98.6 79.7 60.5 60.1 116 112 ...
 $ Creinhardtii_PicSE3                :'data.frame':    12016 obs. of  12 variables:
  ..$ query        : chr [1:12016] "Crei_CR00G00030" "Crei_CR00G00420" "Crei_CR00G00420" "Crei_CR00G00420" ...
  ..$ db           : chr [1:12016] "PicS_PI00G41130" "PicS_PI00G47840" "PicS_PI00G48460" "PicS_PI00G45350" ...
  ..$ perc_identity: num [1:12016] 29.3 34.7 33.5 34.6 32.3 35.5 35.2 61.6 37.2 31.5 ...
  ..$ length       : int [1:12016] 491 196 212 234 217 203 401 99 586 241 ...
  ..$ mismatches   : int [1:12016] 246 122 116 126 134 121 222 37 245 131 ...
  ..$ gap_open     : int [1:12016] 20 4 5 9 5 4 8 1 10 5 ...
  ..$ qstart       : int [1:12016] 1061 296 284 279 278 290 51 31 153 441 ...
  ..$ qend         : int [1:12016] 1547 490 493 494 490 490 421 128 727 664 ...
  ..$ tstart       : int [1:12016] 175 1 401 224 248 555 281 20 16 226 ...
  ..$ tend         : int [1:12016] 568 191 589 448 455 749 673 118 489 449 ...
  ..$ evalue       : num [1:12016] 1.24e-26 7.41e-30 2.45e-28 8.84e-26 5.91e-25 ...
  ..$ bitscore     : num [1:12016] 115 115 119 109 107 108 209 124 333 87.4 ...
 $ Creinhardtii_Ppatens               :'data.frame':    18970 obs. of  12 variables:
  ..$ query        : chr [1:18970] "Crei_CR00G00030" "Crei_CR00G00030" "Crei_CR00G00420" "Crei_CR00G00420" ...
  ..$ db           : chr [1:18970] "Ppat_PP00300G00310" "Ppat_PP00152G00740" "Ppat_PP00043G00850" "Ppat_PP00172G00420" ...
  ..$ perc_identity: num [1:18970] 31.4 29.4 34.3 35.4 35.5 36 38.2 54 37.9 24.2 ...
  ..$ length       : int [1:18970] 525 463 201 209 200 200 212 126 573 392 ...
  ..$ mismatches   : int [1:18970] 271 243 110 114 108 105 111 55 244 223 ...
  ..$ gap_open     : int [1:18970] 25 17 5 4 4 5 8 2 9 7 ...
  ..$ qstart       : int [1:18970] 1097 1097 291 292 292 293 288 5 159 341 ...
  ..$ qend         : int [1:18970] 1569 1542 490 499 490 490 496 129 727 728 ...
  ..$ tstart       : int [1:18970] 142 282 368 246 245 249 1423 2 45 181 ...
  ..$ tend         : int [1:18970] 629 677 547 434 424 427 1617 125 509 502 ...
  ..$ evalue       : num [1:18970] 2.50e-30 1.77e-25 2.20e-28 6.95e-28 1.25e-27 ...
  ..$ bitscore     : num [1:18970] 129 114 120 117 116 113 116 137 346 78.2 ...
 $ Creinhardtii_Vcarteri              :'data.frame':    25447 obs. of  12 variables:
  ..$ query        : chr [1:25447] "Crei_CR00G00050" "Crei_CR00G00090" "Crei_CR00G00200" "Crei_CR00G00200" ...
  ..$ db           : chr [1:25447] "Vcar_VC00G50340" "Vcar_VC00G58610" "Vcar_VC00G133710" "Vcar_VC00G108940" ...
  ..$ perc_identity: num [1:25447] 46.3 52.6 64.3 62.3 60.5 48.2 30 32 46.6 32 ...
  ..$ length       : int [1:25447] 123 232 84 69 81 112 547 507 191 413 ...
  ..$ mismatches   : int [1:25447] 57 87 26 22 31 38 161 182 81 142 ...
  ..$ gap_open     : int [1:25447] 2 4 1 1 1 1 13 15 5 9 ...
  ..$ qstart       : int [1:25447] 246 482 1 1 3 393 30 26 321 31 ...
  ..$ qend         : int [1:25447] 361 711 80 65 82 504 508 514 505 443 ...
  ..$ tstart       : int [1:25447] 511 103 263 241 233 144 627 418 89 634 ...
  ..$ tend         : int [1:25447] 631 313 346 309 313 235 1019 779 264 907 ...
  ..$ evalue       : num [1:25447] 4.53e-18 1.88e-59 4.70e-27 5.44e-20 4.01e-28 ...
  ..$ bitscore     : num [1:25447] 86.3 220 102 82 108 95.9 196 172 154 148 ...
 $ Csubellipsoidea_Aprotothecoides    :'data.frame':    9807 obs. of  12 variables:
  ..$ query        : chr [1:9807] "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" ...
  ..$ db           : chr [1:9807] "Apro_AP00G43730" "Apro_AP00G03030" "Apro_AP00G57210" "Apro_AP00G42580" ...
  ..$ perc_identity: num [1:9807] 43.8 39.2 40.7 42.2 36.7 31.5 42 29.5 30.5 43.8 ...
  ..$ length       : int [1:9807] 240 240 248 206 215 594 300 533 511 242 ...
  ..$ mismatches   : int [1:9807] 132 145 135 110 134 333 173 358 341 134 ...
  ..$ gap_open     : int [1:9807] 2 1 2 1 2 11 1 6 7 1 ...
  ..$ qstart       : int [1:9807] 1 1 1 28 1 13 292 89 100 355 ...
  ..$ qend         : int [1:9807] 239 239 238 224 215 594 590 603 600 594 ...
  ..$ tstart       : int [1:9807] 538 1126 293 524 1217 57 471 15 864 390 ...
  ..$ tend         : int [1:9807] 775 1365 538 729 1429 588 770 547 1370 631 ...
  ..$ evalue       : num [1:9807] 5.13e-58 8.33e-57 1.15e-56 1.71e-48 8.36e-42 ...
  ..$ bitscore     : num [1:9807] 194 192 187 167 149 231 234 207 208 197 ...
 $ Csubellipsoidea_Asterochlorissp    :'data.frame':    13094 obs. of  12 variables:
  ..$ query        : chr [1:13094] "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" ...
  ..$ db           : chr [1:13094] "Aste_AC00G83270" "Aste_AC00G33800" "Aste_AC00G92850" "Aste_AC00G14590" ...
  ..$ perc_identity: num [1:13094] 40.6 41.6 37.4 37.2 35.7 30.6 32 34.6 28.1 28.3 ...
  ..$ length       : int [1:13094] 244 226 238 258 258 559 515 379 534 533 ...
  ..$ mismatches   : int [1:13094] 143 129 149 145 146 365 329 240 318 326 ...
  ..$ gap_open     : int [1:13094] 1 2 0 2 3 6 6 3 7 6 ...
  ..$ qstart       : int [1:13094] 1 1 1 1 1 57 100 224 109 102 ...
  ..$ qend         : int [1:13094] 242 225 238 241 240 596 594 594 594 588 ...
  ..$ tstart       : int [1:13094] 244 325 1001 308 344 10 84 105 100 54 ...
  ..$ tend         : int [1:13094] 487 548 1238 565 599 564 597 483 615 576 ...
  ..$ evalue       : num [1:13094] 2.08e-61 1.81e-57 7.64e-53 6.98e-52 3.40e-47 ...
  ..$ bitscore     : num [1:13094] 199 191 182 176 165 231 233 219 192 190 ...
 $ Csubellipsoidea_Bprasinos          :'data.frame':    7870 obs. of  12 variables:
  ..$ query        : chr [1:7870] "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" ...
  ..$ db           : chr [1:7870] "Bpra_BPRRCC1105_13G00560" "Bpra_BPRRCC1105_12G00090" "Bpra_BPRRCC1105_02G05570" "Bpra_BPRRCC1105_18G00020" ...
  ..$ perc_identity: num [1:7870] 40.1 38.8 32.2 24.9 25.9 42.6 37.4 27.3 26.6 28.3 ...
  ..$ length       : int [1:7870] 242 242 276 213 243 340 294 662 507 446 ...
  ..$ mismatches   : int [1:7870] 143 131 136 138 133 177 173 361 350 258 ...
  ..$ gap_open     : int [1:7870] 1 5 3 7 9 7 2 20 10 7 ...
  ..$ qstart       : int [1:7870] 1 1 1 1 14 275 312 16 110 219 ...
  ..$ qend         : int [1:7870] 242 226 225 197 219 596 594 587 603 603 ...
  ..$ tstart       : int [1:7870] 454 454 537 470 92 331 396 776 899 391 ...
  ..$ tend         : int [1:7870] 693 694 812 676 324 670 689 1407 1396 835 ...
  ..$ evalue       : num [1:7870] 1.34e-60 9.00e-46 2.51e-40 1.77e-10 1.02e-09 ...
  ..$ bitscore     : num [1:7870] 201 161 145 58.9 56.2 239 200 169 169 167 ...
 $ Csubellipsoidea_Chlorellasp        :'data.frame':    11984 obs. of  12 variables:
  ..$ query        : chr [1:11984] "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" ...
  ..$ db           : chr [1:11984] "Chlo_CNC64A_014G02010" "Chlo_CNC64A_021G00640" "Chlo_CNC64A_003G04480" "Chlo_CNC64A_015G00110" ...
  ..$ perc_identity: num [1:11984] 41.8 43.1 44.3 38.2 39 43.3 43.9 29.3 29.9 27.8 ...
  ..$ length       : int [1:11984] 239 239 221 241 236 337 280 564 551 634 ...
  ..$ mismatches   : int [1:11984] 136 133 123 139 143 183 151 335 328 390 ...
  ..$ gap_open     : int [1:11984] 2 2 0 2 1 6 4 10 7 10 ...
  ..$ qstart       : int [1:11984] 1 1 18 5 4 270 320 91 100 28 ...
  ..$ qend         : int [1:11984] 238 238 238 238 238 600 594 593 594 602 ...
  ..$ tstart       : int [1:11984] 369 588 338 329 382 496 990 84 108 1 ...
  ..$ tend         : int [1:11984] 605 824 558 566 617 830 1268 644 656 625 ...
  ..$ evalue       : num [1:11984] 9.40e-59 1.29e-58 3.88e-57 1.69e-51 2.00e-51 ...
  ..$ bitscore     : num [1:11984] 195 197 194 174 175 248 222 206 195 187 ...
 $ Csubellipsoidea_Creinhardtii       :'data.frame':    12169 obs. of  12 variables:
  ..$ query        : chr [1:12169] "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" ...
  ..$ db           : chr [1:12169] "Crei_CR10G05460" "Crei_CR17G06430" "Crei_CR17G06420" "Crei_CR17G06950" ...
  ..$ perc_identity: num [1:12169] 43.8 40.3 39.9 40 40.4 33.3 32 36 33.9 33.2 ...
  ..$ length       : int [1:12169] 240 243 243 240 250 493 513 383 499 509 ...
  ..$ mismatches   : int [1:12169] 133 145 146 142 142 322 333 242 315 305 ...
  ..$ gap_open     : int [1:12169] 2 0 0 1 2 5 6 2 9 12 ...
  ..$ qstart       : int [1:12169] 1 1 1 1 1 107 96 220 107 107 ...
  ..$ qend         : int [1:12169] 239 243 243 240 243 594 599 599 594 594 ...
  ..$ tstart       : int [1:12169] 564 1163 1180 628 598 311 380 486 906 923 ...
  ..$ tend         : int [1:12169] 802 1405 1422 865 847 801 885 868 1400 1417 ...
  ..$ evalue       : num [1:12169] 1.76e-61 9.90e-58 7.47e-56 6.62e-55 4.06e-54 ...
  ..$ bitscore     : num [1:12169] 208 197 192 188 186 234 229 224 226 223 ...
 $ Csubellipsoidea_Csubellipsoidea    :'data.frame':    19275 obs. of  12 variables:
  ..$ query        : chr [1:19275] "Csub_CV00G00010" "Csub_CV00G00020" "Csub_CV00G00030" "Csub_CV00G00040" ...
  ..$ db           : chr [1:19275] "Csub_CV00G00010" "Csub_CV00G00020" "Csub_CV00G00030" "Csub_CV00G00040" ...
  ..$ perc_identity: num [1:19275] 100 100 100 100 100 44 41.6 42.4 40.7 100 ...
  ..$ length       : int [1:19275] 333 209 384 177 244 232 243 238 226 604 ...
  ..$ mismatches   : int [1:19275] 0 0 0 0 0 128 136 135 134 0 ...
  ..$ gap_open     : int [1:19275] 0 0 0 0 0 1 3 1 0 0 ...
  ..$ qstart       : int [1:19275] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ qend         : int [1:19275] 333 209 384 177 244 232 239 238 226 604 ...
  ..$ tstart       : int [1:19275] 1 1 1 1 1 370 355 359 913 1 ...
  ..$ tend         : int [1:19275] 333 209 384 177 244 599 595 594 1138 604 ...
  ..$ evalue       : num [1:19275] 5.40e-238 2.19e-141 6.28e-281 1.88e-124 9.24e-174 ...
  ..$ bitscore     : num [1:19275] 646 391 759 346 476 ...
 $ Csubellipsoidea_Helicosporidiumsp  :'data.frame':    6811 obs. of  12 variables:
  ..$ query        : chr [1:6811] "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" ...
  ..$ db           : chr [1:6811] "Heli_HE0000G01790" "Heli_HE0000G48840" "Heli_HE0000G01540" "Heli_HE0000G18350" ...
  ..$ perc_identity: num [1:6811] 40.1 37.8 38.6 30.8 34.1 36.9 25.9 24.1 43.3 36.6 ...
  ..$ length       : int [1:6811] 269 249 158 195 502 363 205 220 587 481 ...
  ..$ mismatches   : int [1:6811] 132 146 90 117 315 194 140 129 225 291 ...
  ..$ gap_open     : int [1:6811] 3 1 4 7 8 3 8 6 5 4 ...
  ..$ qstart       : int [1:6811] 1 1 1 18 102 267 374 359 6 6 ...
  ..$ qend         : int [1:6811] 240 240 156 197 594 594 569 553 484 474 ...
  ..$ tstart       : int [1:6811] 293 589 317 187 149 197 433 172 2 9 ...
  ..$ tend         : int [1:6811] 561 837 469 378 643 559 634 378 588 487 ...
  ..$ evalue       : num [1:6811] 1.07e-60 6.52e-52 2.72e-24 3.33e-14 1.90e-72 ...
  ..$ bitscore     : num [1:6811] 197 177 97.8 68.6 242 224 65.5 58.2 452 308 ...
 $ Csubellipsoidea_Mpusilla           :'data.frame':    9143 obs. of  12 variables:
  ..$ query        : chr [1:9143] "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" ...
  ..$ db           : chr [1:9143] "Mpus_MP10G04730" "Mpus_MP03G00050" "Mpus_MP03G07490" "Mpus_MP08G02090" ...
  ..$ perc_identity: num [1:9143] 41.2 40.4 39.1 39.3 35.8 33.3 28.3 29.4 41.7 27.1 ...
  ..$ length       : int [1:9143] 226 240 248 224 218 594 646 575 247 613 ...
  ..$ mismatches   : int [1:9143] 131 141 146 126 138 369 379 388 138 357 ...
  ..$ gap_open     : int [1:9143] 1 1 3 3 2 15 9 9 1 7 ...
  ..$ qstart       : int [1:9143] 1 1 1 1 1 28 24 33 359 53 ...
  ..$ qend         : int [1:9143] 226 238 243 217 218 602 594 594 599 585 ...
  ..$ tstart       : int [1:9143] 600 519 369 478 1220 34 68 14 600 92 ...
  ..$ tend         : int [1:9143] 823 758 616 698 1435 619 704 583 846 694 ...
  ..$ evalue       : num [1:9143] 7.33e-57 4.28e-55 4.49e-53 7.70e-43 5.04e-36 ...
  ..$ bitscore     : num [1:9143] 192 187 179 153 134 250 241 219 205 202 ...
 $ Csubellipsoidea_Msp                :'data.frame':    9314 obs. of  12 variables:
  ..$ query        : chr [1:9314] "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" ...
  ..$ db           : chr [1:9314] "Msp_MRCC299_05G00190" "Msp_MRCC299_11G04050" "Msp_MRCC299_03G04480" "Msp_MRCC299_05G02030" ...
  ..$ perc_identity: num [1:9314] 37.4 43.3 39.9 36.5 41.6 31.2 32.5 35.9 28.2 29 ...
  ..$ length       : int [1:9314] 246 238 223 230 209 613 425 412 616 587 ...
  ..$ mismatches   : int [1:9314] 147 122 130 141 94 385 268 233 397 363 ...
  ..$ gap_open     : int [1:9314] 2 5 1 2 4 15 6 9 13 12 ...
  ..$ qstart       : int [1:9314] 1 1 1 1 1 16 175 208 23 54 ...
  ..$ qend         : int [1:9314] 239 226 223 225 182 602 594 597 600 594 ...
  ..$ tstart       : int [1:9314] 512 1006 278 678 1141 328 4 180 154 157 ...
  ..$ tend         : int [1:9314] 757 1242 496 907 1348 929 414 582 762 735 ...
  ..$ evalue       : num [1:9314] 3.21e-55 5.36e-52 4.67e-50 1.47e-46 1.51e-41 ...
  ..$ bitscore     : num [1:9314] 187 179 169 164 149 236 210 214 198 192 ...
 $ Csubellipsoidea_Olucimarinus       :'data.frame':    8396 obs. of  12 variables:
  ..$ query        : chr [1:8396] "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" ...
  ..$ db           : chr [1:8396] "Oluc_OL01G00530" "Oluc_OL01G04730" "Oluc_OL02G00720" "Oluc_OL08G02160" ...
  ..$ perc_identity: num [1:8396] 39.6 38.2 27.9 25.4 23.7 42.3 38.9 30.6 26.6 27.4 ...
  ..$ length       : int [1:8396] 245 246 190 240 194 317 298 523 218 164 ...
  ..$ mismatches   : int [1:8396] 142 139 123 139 127 174 176 324 136 100 ...
  ..$ gap_open     : int [1:8396] 3 6 6 9 7 4 1 12 8 5 ...
  ..$ qstart       : int [1:8396] 1 1 15 14 1 290 308 99 374 374 ...
  ..$ qend         : int [1:8396] 240 234 198 223 192 597 599 593 575 527 ...
  ..$ tstart       : int [1:8396] 391 1000 381 4 319 319 336 736 5 3 ...
  ..$ tend         : int [1:8396] 634 1244 562 233 493 635 633 1247 214 157 ...
  ..$ evalue       : num [1:8396] 7.54e-54 6.87e-44 1.21e-14 5.12e-10 2.55e-08 ...
  ..$ bitscore     : num [1:8396] 181 155 70.9 56.2 52 224 210 192 53.1 47.8 ...
 $ Csubellipsoidea_Omediterraneus     :'data.frame':    8242 obs. of  12 variables:
  ..$ query        : chr [1:8242] "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" ...
  ..$ db           : chr [1:8242] "Omed_OM_01G02190" "Omed_OM_04G04920" "Omed_OM_16G00910" "Omed_OM_10G03000" ...
  ..$ perc_identity: num [1:8242] 37.2 27.6 28.7 24.7 42 38.6 27.6 25.3 24.9 39.8 ...
  ..$ length       : int [1:8242] 266 199 174 194 319 298 649 518 225 467 ...
  ..$ mismatches   : int [1:8242] 134 136 102 125 176 177 377 374 157 265 ...
  ..$ gap_open     : int [1:8242] 7 4 6 7 4 1 16 6 6 5 ...
  ..$ qstart       : int [1:8242] 1 1 1 1 290 308 21 83 361 20 ...
  ..$ qend         : int [1:8242] 234 197 165 192 599 599 593 592 575 474 ...
  ..$ tstart       : int [1:8242] 1133 483 173 451 324 340 769 788 31 32 ...
  ..$ tend         : int [1:8242] 1397 675 333 625 642 637 1400 1300 253 494 ...
  ..$ evalue       : num [1:8242] 1.29e-44 5.60e-16 3.27e-10 3.03e-09 6.22e-65 ...
  ..$ bitscore     : num [1:8242] 158 75.1 57.8 55.1 223 208 187 173 55.1 328 ...
 $ Csubellipsoidea_Osp                :'data.frame':    7960 obs. of  12 variables:
  ..$ query        : chr [1:7960] "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" ...
  ..$ db           : chr [1:7960] "Osp_ORCC809_01G06000" "Osp_ORCC809_01G02020" "Osp_ORCC809_02G04170" "Osp_ORCC809_08G02150" ...
  ..$ perc_identity: num [1:7960] 37.1 38.6 26.6 25.8 23.7 41 38.9 27.5 27.9 28.9 ...
  ..$ length       : int [1:7960] 245 241 199 240 194 317 293 639 488 239 ...
  ..$ mismatches   : int [1:7960] 148 118 138 138 127 178 173 380 327 138 ...
  ..$ gap_open     : int [1:7960] 3 4 4 10 7 4 1 13 10 9 ...
  ..$ qstart       : int [1:7960] 1 1 1 14 1 290 308 21 119 359 ...
  ..$ qend         : int [1:7960] 240 212 197 223 192 597 594 587 592 575 ...
  ..$ tstart       : int [1:7960] 353 1087 423 93 319 281 373 723 980 11 ...
  ..$ tend         : int [1:7960] 596 1326 615 322 493 597 665 1350 1456 239 ...
  ..$ evalue       : num [1:7960] 3.35e-51 1.87e-43 2.57e-16 2.35e-10 4.39e-09 ...
  ..$ bitscore     : num [1:7960] 174 154 75.9 57.8 54.3 215 211 185 169 70.5 ...
 $ Csubellipsoidea_Otauri             :'data.frame':    8087 obs. of  12 variables:
  ..$ query        : chr [1:8087] "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" ...
  ..$ db           : chr [1:8087] "Otau_OT_01G04640" "Otau_OT_02G03830" "Otau_OT_08G02310" "Otau_OT_09G03170" ...
  ..$ perc_identity: num [1:8087] 37.5 28.2 24.4 23.7 39.7 37.3 27.7 27 29.6 37.3 ...
  ..$ length       : int [1:8087] 267 188 234 194 300 386 495 659 162 467 ...
  ..$ mismatches   : int [1:8087] 133 125 139 127 171 231 340 369 99 277 ...
  ..$ gap_open     : int [1:8087] 6 5 8 7 3 7 6 19 5 5 ...
  ..$ qstart       : int [1:8087] 1 15 14 1 308 219 110 21 374 20 ...
  ..$ qend         : int [1:8087] 234 198 219 192 599 594 594 593 527 474 ...
  ..$ tstart       : int [1:8087] 1141 422 92 420 224 234 818 777 47 24 ...
  ..$ tend         : int [1:8087] 1406 603 315 594 521 618 1304 1409 201 486 ...
  ..$ evalue       : num [1:8087] 1.69e-44 7.04e-16 4.72e-10 9.77e-08 2.90e-63 ...
  ..$ bitscore     : num [1:8087] 157 74.7 57 50.4 216 218 187 177 52.4 309 ...
 $ Csubellipsoidea_PicRCC4223         :'data.frame':    10154 obs. of  12 variables:
  ..$ query        : chr [1:10154] "Csub_CV00G00010" "Csub_CV00G00050" "Csub_CV00G00050" "Csub_CV00G00050" ...
  ..$ db           : chr [1:10154] "PicR_RCC4223.105g00260" "PicR_RCC4223.04g04750" "PicR_RCC4223.07g01050" "PicR_RCC4223.03g00910" ...
  ..$ perc_identity: num [1:10154] 27 42.9 41 38.9 38.2 39.7 34.2 34.2 32.3 32.8 ...
  ..$ length       : int [1:10154] 304 238 239 239 241 242 579 489 504 503 ...
  ..$ mismatches   : int [1:10154] 185 134 139 146 149 143 373 312 330 329 ...
  ..$ gap_open     : int [1:10154] 11 1 2 0 0 2 5 4 4 6 ...
  ..$ qstart       : int [1:10154] 56 1 1 1 1 1 26 111 98 97 ...
  ..$ qend         : int [1:10154] 333 238 238 239 241 241 601 594 594 592 ...
  ..$ tstart       : int [1:10154] 23 472 597 1190 1084 346 16 80 128 203 ...
  ..$ tend         : int [1:10154] 315 707 834 1428 1324 585 589 563 627 703 ...
  ..$ evalue       : num [1:10154] 1.31e-16 6.85e-63 4.78e-59 8.45e-59 9.87e-58 ...
  ..$ bitscore     : num [1:10154] 79 207 198 199 196 181 315 285 240 229 ...
  [list output truncated]

Synteny network inference

To infer the synteny network, use the function infer_syntenet().

start_time <- Sys.time() 
algae_network <- infer_syntenet(
    blast_list = diamond_list, 
    annotation = pdata$annotation
)
end_time <- Sys.time()

head(algae_network)
                Anchor1               Anchor2
1 Chlo_CNC64A_028G00030 Chlo_CNC64A_035G00060
2 Chlo_CNC64A_028G00040 Chlo_CNC64A_035G00070
3 Chlo_CNC64A_028G00070 Chlo_CNC64A_035G00080
4 Chlo_CNC64A_028G00080 Chlo_CNC64A_035G00090
5 Chlo_CNC64A_028G00110 Chlo_CNC64A_035G00140
6 Chlo_CNC64A_028G00140 Chlo_CNC64A_035G00150

How long did it take?

end_time - start_time
Time difference of 45.14361 secs

Network clustering

The function cluster_network() is used to assign each gene to a unique cluster using the Infomap algorithm.

clusters <- cluster_network(algae_network)
head(clusters)
                   Gene Cluster
1 Chlo_CNC64A_028G00030       1
2 Chlo_CNC64A_028G00040       2
3 Chlo_CNC64A_028G00070       3
4 Chlo_CNC64A_028G00080       4
5 Chlo_CNC64A_028G00110       5
6 Chlo_CNC64A_028G00140       6

Phylogenomic profiling

The function phylogenomic_profile() groups synteny clusters using Ward’s clustering on a matrix of Jaccard distances.

Warning

Calculating Jaccard similarity indices uses vegan::vegdist(), which temporarily creates a long vector that uses considerable memory.

To avoid issues, let’s load the pre-computed output from phylogenomic_profile().

load(here::here("data", "profiles.rda"))

Phylogenomic profiles can be generated with:

profiles <- phylogenomic_profile(clusters)

Phylogenomic profiling

Inspecting the output of phylogenomic_profile():

dplyr::glimpse(profiles)
List of 2
 $ profile_matrix: int [1:22607, 1:16] 0 0 0 0 0 0 0 0 0 0 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:22607] "12323" "12322" "12321" "12320" ...
  .. ..$ : chr [1:16] "Apro" "Aste" "Bpra" "Chlo" ...
 $ hclust        :List of 7
  ..$ merge      : int [1:22606, 1:2] -4 -7 -9 -18 -19 -20 -21 -22 -11 -13 ...
  ..$ height     : num [1:22606] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ order      : int [1:22607] 12323 12322 12321 12320 12319 12318 12317 12316 12315 12314 ...
  ..$ labels     : chr [1:22607] "1" "2" "3" "4" ...
  ..$ method     : chr "ward.D"
  ..$ call       : language stats::hclust(d = dist_mat, method = "ward.D")
  ..$ dist.method: chr "jaccard"
  ..- attr(*, "class")= chr "hclust"
profiles$profile_matrix[1:10, 1:10]
       
        Apro Aste Bpra Chlo Crei Csub Mpus Msp Oluc Omed
  12323    0    0    0    0    1    0    0   0    0    0
  12322    0    0    0    0    1    0    0   0    0    0
  12321    0    0    0    0    1    0    0   0    0    0
  12320    0    0    0    0    1    0    0   0    0    0
  12319    0    0    0    0    1    0    0   0    0    0
  12318    0    0    0    0    1    0    0   0    0    0
  12317    0    0    0    0    1    0    0   0    0    0
  12316    0    0    0    0    1    0    0   0    0    0
  12315    0    0    0    0    1    0    0   0    0    0
  12314    0    0    0    0    1    0    0   0    0    0

Visualizing phylogenomic profiles

Profiles can be visualized as a heatmap or as a network.

First, let’s create a data frame of species taxonomy (row annotation) for the heatmap.

# Create a data frame of taxonomic information for each species
species_info <- data.frame(
    Species = c(
        "Aprotothecoides", "Chlorellasp", "PicRCC4223", 
        "PicSE3", "Asterochlorissp", "Csubellipsoidea", "Creinhardtii", 
        "Vcarteri", "Bprasinos", "Otauri", "Osp", "Olucimarinus", 
        "Omediterraneus", "Msp", "Mpusilla", "Ppatens"
    ),
    Abbrev = c(
        "Apro", "Chlo", "PicR", "PicS", "Aste", "Csub", "Crei",
        "Vcar", "Bpra", "Otau", "Osp", "Oluc", "Omed", "Msp", 
        "Mpus", "Ppat" 
    ),
    Clade = c(
        rep("Trebouxiophyceae", 6), 
        rep("Chlamydomonadales", 2),
        rep("Marmiellales", 7), 
        "Outgroup"
    )
)

# Reorder columns and replace abbreviations with species names
profiles$profile_matrix <- profiles$profile_matrix[, species_info$Abbrev]
colnames(profiles$profile_matrix) <- species_info$Species

Visualizing phylogenomic profiles

To visualize profiles as a heatmap, use the function plot_profiles().

species_annotation <- species_info[, c("Species", "Clade")]
plot_profiles(
    profiles, 
    species_annotation = species_annotation,
    cluster_species = species_info$Species
)

Visualizing phylogenomic profiles

To visualize clusters as a network, use the function plot_network().

plot_network(
    algae_network, 
    clusters, 
    cluster_id = clusters$Cluster[1:5]
)

Visualizing phylogenomic profiles

Networks can also be visualized interactively.

plot_network(
    algae_network, 
    clusters, cluster_id = clusters$Cluster[1:5], 
    interactive = TRUE, dim_interactive = c(1500, 500)
)

Visualizing phylogenomic profiles

Nodes can be colored using custom annotation.

genes <- unique(c(algae_network$Anchor1, algae_network$Anchor2))
gene_annotation <- data.frame(
    Gene = genes,
    Abbrev = unlist(lapply(strsplit(genes, "_"), head, 1))
) |>
    merge(x = _, y = species_info) |>
    dplyr::select(Gene, Clade)
head(gene_annotation)
             Gene            Clade
1 Apro_AP00G07470 Trebouxiophyceae
2 Apro_AP00G07440 Trebouxiophyceae
3 Apro_AP00G38810 Trebouxiophyceae
4 Apro_AP00G18930 Trebouxiophyceae
5 Apro_AP00G38780 Trebouxiophyceae
6 Apro_AP00G35340 Trebouxiophyceae

Visualizing phylogenomic profiles

Nodes can be colored using custom annotation.

plot_network(
    algae_network, 
    clusters, 
    cluster_id = clusters$Cluster[1:5], 
    color_by = gene_annotation
)

Microsynteny-based phylogeny inference

To infer a phylogeny, the matrix of phylogenomic profiles must be binarized and transposed with binarize_and_transpose().

bt_mat <- binarize_and_transpose(profiles$profile_matrix)
bt_mat[1:5, 1:5]
                 
                  12323 12322 12321 12320 12319
  Aprotothecoides     0     0     0     0     0
  Chlorellasp         0     0     0     0     0
  PicRCC4223          0     0     0     0     0
  PicSE3              0     0     0     0     0
  Asterochlorissp     0     0     0     0     0

Then, you can:

  1. Use profiles2phylip() to write the transposed binary matrix to a PHYLIP file and run IQTREE2 (or something similar) from the command line;

  2. Use the helper function infer_microsynteny_phylogeny(), which allows you to run IQTREE2 from an R session.

Microsynteny-based phylogeny inference

infer_microsynteny_phylogeny() infers a phylogeny with IQTREE2 and returns the path to output files (tempdir() by default).

if(iqtree_is_installed()) {
    phylo <- infer_microsynteny_phylogeny(
        bt_mat, 
        outgroup = "Ppatens", 
        model = "MK+ASC+R",
        threads = 1
    )
}
phylo
 [1] "/tmp/RtmpGuKpNr/microsynteny_phylogeny_12_Sep_2022_10h49.phy"           
 [2] "/tmp/RtmpGuKpNr/microsynteny_phylogeny_12_Sep_2022_10h49.phy.bionj"     
 [3] "/tmp/RtmpGuKpNr/microsynteny_phylogeny_12_Sep_2022_10h49.phy.ckp.gz"    
 [4] "/tmp/RtmpGuKpNr/microsynteny_phylogeny_12_Sep_2022_10h49.phy.contree"   
 [5] "/tmp/RtmpGuKpNr/microsynteny_phylogeny_12_Sep_2022_10h49.phy.iqtree"    
 [6] "/tmp/RtmpGuKpNr/microsynteny_phylogeny_12_Sep_2022_10h49.phy.log"       
 [7] "/tmp/RtmpGuKpNr/microsynteny_phylogeny_12_Sep_2022_10h49.phy.mldist"    
 [8] "/tmp/RtmpGuKpNr/microsynteny_phylogeny_12_Sep_2022_10h49.phy.parstree"  
 [9] "/tmp/RtmpGuKpNr/microsynteny_phylogeny_12_Sep_2022_10h49.phy.splits.nex"
[10] "/tmp/RtmpGuKpNr/microsynteny_phylogeny_12_Sep_2022_10h49.phy.treefile"

Phylogeny visualization

You can read the .treefile file from infer_microsynteny_phylogeny() with the function read.tree() from the treeio package and visualize it with the ggtree package.

library(ggtree)
algae_tree <- read.tree(phylo[10])
ggtree(algae_tree) +
    geom_tiplab(size = 3) +
    xlim(0, 0.2)

Here’s where you can find me:






@almeidasilvaf

almeidasilvaf

almeidasilvaf.github.io

Fabricio Almeida-Silva

0000-0002-5314-2964

Part 2

Fabricio Almeida-Silva @almeidasilvaf